Variant chr10-126004905-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_145235.5(FANK1):c.561G>A(p.Ala187=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0065 in 1,614,090 control chromosomes in the GnomAD database, including 50 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0054 ( 4 hom., cov: 32)

Exomes 𝑓: 0.0066 ( 46 hom. )

Consequence

FANK1
NM_145235.5 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0170

Variant links:

Genes affected

FANK1 (HGNC:23527): (fibronectin type III and ankyrin repeat domains 1) Involved in regulation of apoptotic process and regulation of transcription, DNA-templated. Located in cytosol and nucleoplasm. Colocalizes with chromatin. [provided by Alliance of Genome Resources, Apr 2022]

FANK1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.6).

BP6

Variant 10-126004905-G-A is Benign according to our data. Variant chr10-126004905-G-A is described in ClinVar as [Benign]. Clinvar id is 778475.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.017 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
FANK1	NM_145235.5 linkuse as main transcript	c.561G>A	p.Ala187=	synonymous_variant	7/11	ENST00000368693.6
FANK1	NM_001350939.2 linkuse as main transcript	c.639G>A	p.Ala213=	synonymous_variant	8/12
FANK1	NM_001363549.2 linkuse as main transcript	c.543G>A	p.Ala181=	synonymous_variant	7/11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FANK1	ENST00000368693.6 linkuse as main transcript	c.561G>A	p.Ala187=	synonymous_variant	7/11	1	NM_145235.5	P1	Q8TC84-1

Frequencies

GnomAD3 genomes

AF:

0.00544

AC:

827

AN:

152126

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00150

Gnomad AMI

AF:

0.00549

Gnomad AMR

AF:

0.00753

Gnomad ASJ

AF:

0.0127

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00415

Gnomad FIN

AF:

0.000377

Gnomad MID

AF:

0.00955

Gnomad NFE

AF:

0.00828

Gnomad OTH

AF:

0.00527

GnomAD3 exomes

AF:

0.00527

AC:

1326

AN:

251450

Hom.:

AF XY:

0.00544

AC XY:

739

AN XY:

135896

show subpopulations

Gnomad AFR exome

AF:

0.00135

Gnomad AMR exome

AF:

0.00532

Gnomad ASJ exome

AF:

0.0146

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00480

Gnomad FIN exome

AF:

0.000647

Gnomad NFE exome

AF:

0.00673

Gnomad OTH exome

AF:

0.00766

GnomAD4 exome

AF:

0.00661

AC:

9664

AN:

1461846

Hom.:

Cov.:

AF XY:

0.00656

AC XY:

4774

AN XY:

727214

show subpopulations

Gnomad4 AFR exome

AF:

0.00137

Gnomad4 AMR exome

AF:

0.00570

Gnomad4 ASJ exome

AF:

0.0132

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00441

Gnomad4 FIN exome

AF:

0.000861

Gnomad4 NFE exome

AF:

0.00727

Gnomad4 OTH exome

AF:

0.00793

GnomAD4 genome

AF:

0.00543

AC:

826

AN:

152244

Hom.:

Cov.:

AF XY:

0.00485

AC XY:

361

AN XY:

74426

show subpopulations

Gnomad4 AFR

AF:

0.00149

Gnomad4 AMR

AF:

0.00752

Gnomad4 ASJ

AF:

0.0127

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00415

Gnomad4 FIN

AF:

0.000377

Gnomad4 NFE

AF:

0.00826

Gnomad4 OTH

AF:

0.00522

Alfa

AF:

0.00693

Hom.:

Bravo

AF:

0.00549

Asia WGS

AF:

0.000866

AC:

AN:

3478

EpiCase

AF:

0.00872

EpiControl

AF:

0.00865

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jun 15, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

0.45

DANN

Benign

0.63

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over