5-149279585-G-T

Variant names:

• chr5-149279585-G-T
• rs11954165
• NM_152406.4:c.16+7601G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000296721.9(AFAP1L1):​c.16+7601G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0753 in 152,240 control chromosomes in the GnomAD database, including 569 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 0.075 (569 hom., cov: 33)
• Consequence: AFAP1L1 ENST00000296721.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.121
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000296721.9. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AFAP1L1	NM_152406.4	MANE Select	c.16+7601G>T		intron	N/A	NP_689619.1
	AFAP1L1	NM_001323062.2		c.16+7601G>T		intron	N/A	NP_001309991.1
	AFAP1L1	NM_001146337.3		c.16+7601G>T		intron	N/A	NP_001139809.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AFAP1L1	ENST00000296721.9	TSL:1 MANE Select	c.16+7601G>T		intron	N/A	ENSP00000296721.4
	AFAP1L1	ENST00000515000.1	TSL:1	c.16+7601G>T		intron	N/A	ENSP00000424427.1
	AFAP1L1	ENST00000455574.6	TSL:1	n.114+7601G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0753 AC: 11453 AN: 152122 Hom.: 570 Cov.: 33

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.0436

Gnomad ASJ AF: 0.0481

Gnomad EAS AF: 0.0154

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0228

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0594

Gnomad OTH AF: 0.0770

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

GnomAD4 genome AF: 0.0753 AC: 11460 AN: 152240 Hom.: 569 Cov.: 33 AF XY: 0.0729 AC XY: 5427 AN XY: 74440

African (AFR) AF: 0.133 AC: 5542 AN: 41518

American (AMR) AF: 0.0436 AC: 666 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0481 AC: 167 AN: 3470

East Asian (EAS) AF: 0.0154 AC: 80 AN: 5182

South Asian (SAS) AF: 0.103 AC: 496 AN: 4828

European-Finnish (FIN) AF: 0.0228 AC: 242 AN: 10608

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0594 AC: 4042 AN: 68024

Other (OTH) AF: 0.0762 AC: 161 AN: 2114

Alfa AF: 0.0590 Hom.: 400

Bravo AF: 0.0787

Asia WGS AF: 0.0590 AC: 204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.7
DANN	Benign	0.65
PhyloP100		0.12
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11954165; hg19: chr5-148659148;