Variant 5-149278347-C-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_152406.4(AFAP1L1):c.16+6363C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 151,858 control chromosomes in the GnomAD database, including 21,726 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.53 ( 21726 hom., cov: 31)

Consequence

AFAP1L1
NM_152406.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.184

Variant links:

Genes affected

AFAP1L1 (HGNC:26714): (actin filament associated protein 1 like 1) Predicted to enable SH3 domain binding activity. Predicted to be located in cell junction; cell projection; and podosome. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

AFAP1L1 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 (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.754 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AFAP1L1	NM_152406.4 linkuse as main transcript	c.16+6363C>A		intron_variant		ENST00000296721.9	NP_689619.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
AFAP1L1	ENST00000296721.9 linkuse as main transcript	c.16+6363C>A	intron_variant	1	NM_152406.4	ENSP00000296721	P1	Q8TED9-1
AFAP1L1	ENST00000515000.1 linkuse as main transcript	c.16+6363C>A	intron_variant	1		ENSP00000424427		Q8TED9-2
AFAP1L1	ENST00000455574.6 linkuse as main transcript	n.114+6363C>A	intron_variant, non_coding_transcript_variant	1
AFAP1L1	ENST00000522492.1 linkuse as main transcript	n.90+6363C>A	intron_variant, non_coding_transcript_variant	3

Frequencies

GnomAD3 genomes

AF:

0.529

AC:

80208

AN:

151738

Hom.:

21694

Cov.:

show subpopulations

Gnomad AFR

AF:

0.441

Gnomad AMI

AF:

0.471

Gnomad AMR

AF:

0.616

Gnomad ASJ

AF:

0.539

Gnomad EAS

AF:

0.774

Gnomad SAS

AF:

0.589

Gnomad FIN

AF:

0.515

Gnomad MID

AF:

0.576

Gnomad NFE

AF:

0.541

Gnomad OTH

AF:

0.535

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.529

AC:

80280

AN:

151858

Hom.:

21726

Cov.:

AF XY:

0.530

AC XY:

39339

AN XY:

74200

show subpopulations

Gnomad4 AFR

AF:

0.441

Gnomad4 AMR

AF:

0.617

Gnomad4 ASJ

AF:

0.539

Gnomad4 EAS

AF:

0.774

Gnomad4 SAS

AF:

0.591

Gnomad4 FIN

AF:

0.515

Gnomad4 NFE

AF:

0.541

Gnomad4 OTH

AF:

0.537

Alfa

AF:

0.540

Hom.:

35618

Bravo

AF:

0.535

Asia WGS

AF:

0.667

AC:

2321

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.1

DANN

Benign

0.83

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