rs10044242

Variant names:

• chr5-149326736-C-G
• rs10044242
• NM_152406.4:c.1811-2930C>G

Your query was ambiguous. Multiple possible variants found:

• chr5-149326736-C-G
• chr5-149326736-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_152406.4(AFAP1L1):​c.1811-2930C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0114 in 152,070 control chromosomes in the GnomAD database, including 19 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 0.011 (19 hom., cov: 32)
• Consequence: AFAP1L1 NM_152406.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292
• Publications: 5 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]

ENSG00000285736 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0114 (1737/152070) while in subpopulation AFR AF = 0.0235 (976/41480). AF 95% confidence interval is 0.0223. There are 19 homozygotes in GnomAd4. There are 783 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 19 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AFAP1L1	NM_152406.4	c.1811-2930C>G		intron_variant	Intron 15 of 18	ENST00000296721.9	NP_689619.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AFAP1L1	ENST00000296721.9	c.1811-2930C>G		intron_variant	Intron 15 of 18	1	NM_152406.4	ENSP00000296721.4
AFAP1L1	ENST00000515000.1	c.1811-2930C>G		intron_variant	Intron 15 of 17	1		ENSP00000424427.1
AFAP1L1	ENST00000513665.1	n.972-2930C>G		intron_variant	Intron 6 of 9	2
ENSG00000285736	ENST00000648705.2	n.176-1822G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0114 AC: 1729 AN: 151952 Hom.: 19 Cov.: 32

Gnomad AFR AF: 0.0234

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.00642

Gnomad ASJ AF: 0.00404

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00166

Gnomad FIN AF: 0.00199

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00860

Gnomad OTH AF: 0.0139

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

GnomAD4 genome AF: 0.0114 AC: 1737 AN: 152070 Hom.: 19 Cov.: 32 AF XY: 0.0105 AC XY: 783 AN XY: 74328

African (AFR) AF: 0.0235 AC: 976 AN: 41480

American (AMR) AF: 0.00641 AC: 98 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00404 AC: 14 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.00167 AC: 8 AN: 4804

European-Finnish (FIN) AF: 0.00199 AC: 21 AN: 10556

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00860 AC: 585 AN: 67984

Other (OTH) AF: 0.0138 AC: 29 AN: 2108

Alfa AF: 0.0107 Hom.: 0

Bravo AF: 0.0127

Asia WGS AF: 0.00375 AC: 13 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	4.5
DANN	Benign	0.91
PhyloP100		-0.29
Mutation Taster		=100/0	polymorphism

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: rs10044242; hg19: chr5-148706299;