5-149285867-C-T

Variant names:

• chr5-149285867-C-T
• rs352355
• NM_152406.4:c.17-13642C>T

Variant summary

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

The NM_152406.4(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 NM_152406.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.801
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152406.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AFAP1L1	NM_152406.4	MANE Select	c.17-13642C>T		intron	N/A	NP_689619.1	Q8TED9-1
	AFAP1L1	NM_001323062.2		c.17-13642C>T		intron	N/A	NP_001309991.1
	AFAP1L1	NM_001146337.3		c.17-13642C>T		intron	N/A	NP_001139809.1	Q8TED9-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AFAP1L1	ENST00000296721.9	TSL:1 MANE Select	c.17-13642C>T		intron	N/A	ENSP00000296721.4	Q8TED9-1
	AFAP1L1	ENST00000515000.1	TSL:1	c.17-13642C>T		intron	N/A	ENSP00000424427.1	Q8TED9-2
	AFAP1L1	ENST00000455574.6	TSL:1	n.115-13642C>T		intron	N/A

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

African (AFR) AF: 0.516 AC: 21312 AN: 41280

American (AMR) AF: 0.831 AC: 12657 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.844 AC: 2925 AN: 3466

East Asian (EAS) AF: 0.795 AC: 4080 AN: 5130

South Asian (SAS) AF: 0.859 AC: 4127 AN: 4804

European-Finnish (FIN) AF: 0.904 AC: 9525 AN: 10532

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.880 AC: 59719 AN: 67834

Other (OTH) AF: 0.769 AC: 1617 AN: 2104

Alfa AF: 0.847 Hom.: 93046

Bravo AF: 0.756

Asia WGS AF: 0.814 AC: 2827 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.50
PhyloP100		-0.80
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: rs352355; hg19: chr5-148665430;