rs10044242

chr5-149326736-C-Gchr5-149326736-C-T

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 19 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AFAP1L1	NM_152406.4	c.1811-2930C>G		intron_variant		ENST00000296721.9
LOC124901103	XR_007058989.1	n.215-1822G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AFAP1L1	ENST00000296721.9	c.1811-2930C>G		intron_variant		1	NM_152406.4	P1
AFAP1L1	ENST00000515000.1	c.1811-2930C>G		intron_variant		1
	ENST00000648705.1	n.163-1822G>C		intron_variant, non_coding_transcript_variant
AFAP1L1	ENST00000513665.1	n.972-2930C>G		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.0235

Gnomad4 AMR AF: 0.00641

Gnomad4 ASJ AF: 0.00404

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00167

Gnomad4 FIN AF: 0.00199

Gnomad4 NFE AF: 0.00860

Gnomad4 OTH AF: 0.0138

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

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: rs10044242; hg19: chr5-148706299;