5-149285867-C-T

Position:

• chr5-149285867-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000296721.9(AFAP1L1):​c.17-13642C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.772 in 151,570 control chromosomes in the GnomAD database, including 47,155 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 0.77 (47155 hom., cov: 31)
• Consequence: AFAP1L1 ENST00000296721.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.801

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AFAP1L1	NM_152406.4	c.17-13642C>T		intron_variant		ENST00000296721.9	NP_689619.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AFAP1L1	ENST00000296721.9	c.17-13642C>T		intron_variant		1	NM_152406.4	ENSP00000296721	P1
AFAP1L1	ENST00000515000.1	c.17-13642C>T		intron_variant		1		ENSP00000424427
AFAP1L1	ENST00000455574.6	n.115-13642C>T		intron_variant, non_coding_transcript_variant		1
AFAP1L1	ENST00000522492.1	n.91-13642C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.772 AC: 116923 AN: 151450 Hom.: 47132 Cov.: 31

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.917

Gnomad AMR AF: 0.831

Gnomad ASJ AF: 0.844

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.860

Gnomad FIN AF: 0.904

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.772 AC: 116998 AN: 151570 Hom.: 47155 Cov.: 31 AF XY: 0.776 AC XY: 57459 AN XY: 74086

Gnomad4 AFR AF: 0.516

Gnomad4 AMR AF: 0.831

Gnomad4 ASJ AF: 0.844

Gnomad4 EAS AF: 0.795

Gnomad4 SAS AF: 0.859

Gnomad4 FIN AF: 0.904

Gnomad4 NFE AF: 0.880

Gnomad4 OTH AF: 0.769

Alfa AF: 0.858 Hom.: 75130

Bravo AF: 0.756

Asia WGS AF: 0.814 AC: 2827 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.50

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

Other links and lift over

dbSNP: rs352355; hg19: chr5-148665430;