Variant rs9909216 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001377321.1(ABCA10):c.607C>T(p.Pro203Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 1,612,436 control chromosomes in the GnomAD database, including 337,943 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.63 ( 31068 hom., cov: 31)

Exomes 𝑓: 0.65 ( 306875 hom. )

Consequence

ABCA10
NM_001377321.1 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0330

Variant links:

Genes affected

ABCA10 (HGNC:30): (ATP binding cassette subfamily A member 10) The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intracellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, and White). This encoded protein is a member of the ABC1 subfamily. Members of the ABC1 subfamily comprise the only major ABC subfamily found exclusively in multicellular eukaryotes. This gene is clustered among 4 other ABC1 family members on 17q24, but neither the substrate nor the function of this gene is known. [provided by RefSeq, Jul 2008]

ABCA10 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=6.0603534E-6).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABCA10	NM_001377321.1 linkuse as main transcript	c.607C>T	p.Pro203Ser	missense_variant	7/39	ENST00000690296.1	NP_001364250.1
ABCA10	NM_080282.4 linkuse as main transcript	c.607C>T	p.Pro203Ser	missense_variant	8/40		NP_525021.3	Q8WWZ4-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABCA10	ENST00000690296.1 linkuse as main transcript	c.607C>T	p.Pro203Ser	missense_variant	7/39		NM_001377321.1	ENSP00000509702.1		Q8WWZ4-1
ABCA10	ENST00000522406.5 linkuse as main transcript	n.607C>T		non_coding_transcript_exon_variant	7/41	1		ENSP00000429853.1		Q8WWZ4-5

Frequencies

GnomAD3 genomes

AF:

0.635

AC:

96369

AN:

151824

Hom.:

31065

Cov.:

show subpopulations

Gnomad AFR

AF:

0.643

Gnomad AMI

AF:

0.778

Gnomad AMR

AF:

0.593

Gnomad ASJ

AF:

0.542

Gnomad EAS

AF:

0.328

Gnomad SAS

AF:

0.614

Gnomad FIN

AF:

0.633

Gnomad MID

AF:

0.680

Gnomad NFE

AF:

0.667

Gnomad OTH

AF:

0.619

GnomAD3 exomes

AF:

0.614

AC:

153890

AN:

250712

Hom.:

48468

AF XY:

0.618

AC XY:

83770

AN XY:

135522

show subpopulations

Gnomad AFR exome

AF:

0.639

Gnomad AMR exome

AF:

0.588

Gnomad ASJ exome

AF:

0.540

Gnomad EAS exome

AF:

0.309

Gnomad SAS exome

AF:

0.622

Gnomad FIN exome

AF:

0.628

Gnomad NFE exome

AF:

0.668

Gnomad OTH exome

AF:

0.635

GnomAD4 exome

AF:

0.645

AC:

942054

AN:

1460494

Hom.:

306875

Cov.:

AF XY:

0.645

AC XY:

468714

AN XY:

726562

show subpopulations

Gnomad4 AFR exome

AF:

0.640

Gnomad4 AMR exome

AF:

0.589

Gnomad4 ASJ exome

AF:

0.544

Gnomad4 EAS exome

AF:

0.322

Gnomad4 SAS exome

AF:

0.624

Gnomad4 FIN exome

AF:

0.632

Gnomad4 NFE exome

AF:

0.664

Gnomad4 OTH exome

AF:

0.632

GnomAD4 genome

AF:

0.634

AC:

96404

AN:

151942

Hom.:

31068

Cov.:

AF XY:

0.629

AC XY:

46699

AN XY:

74252

show subpopulations

Gnomad4 AFR

AF:

0.643

Gnomad4 AMR

AF:

0.592

Gnomad4 ASJ

AF:

0.542

Gnomad4 EAS

AF:

0.328

Gnomad4 SAS

AF:

0.613

Gnomad4 FIN

AF:

0.633

Gnomad4 NFE

AF:

0.667

Gnomad4 OTH

AF:

0.616

Alfa

AF:

0.647

Hom.:

79997

Bravo

AF:

0.628

TwinsUK

AF:

0.669

AC:

2480

ALSPAC

AF:

0.661

AC:

2548

ESP6500AA

AF:

0.649

AC:

2861

ESP6500EA

AF:

0.658

AC:

5656

ExAC

AF:

0.621

AC:

75369

Asia WGS

AF:

0.493

AC:

1714

AN:

3478

EpiCase

AF:

0.668

EpiControl

AF:

0.666

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.59

BayesDel_noAF

Benign

-0.48

CADD

Benign

9.9

DANN

Benign

0.31

DEOGEN2

Benign

0.032

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.029

LIST_S2

Benign

0.40

MetaRNN

Benign

0.0000061

MetaSVM

Benign

-0.97

MutationAssessor

Benign

0.55

PrimateAI

Benign

0.24

PROVEAN

Benign

-0.15

REVEL

Benign

0.099

Sift

Benign

0.44

Sift4G

Benign

0.56

Polyphen

0.0060

Vest4

0.041

MPC

0.030

ClinPred

0.0096

GERP RS

2.4

Varity_R

0.044

gMVP

0.050

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over