rs3181224

Variant names:

• chr5-159313842-A-G
• rs3181224
• ENST00000521472.6:n.289+2428A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-159313842-A-G
• chr5-159313842-A-T

Variant summary

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

The ENST00000521472.6(ENSG00000249738):​n.289+2428A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,282 control chromosomes in the GnomAD database, including 842 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 0.10 (842 hom., cov: 32)
• Consequence: ENSG00000249738 ENST00000521472.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.543
• Publications: 29 publications found

Genes affected

ENSG00000249738 (HGNC:58156):

LOC105377683 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377683	XR_941138.3	n.401-1376A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249738	ENST00000521472.6	n.289+2428A>G		intron_variant	Intron 2 of 3	3
ENSG00000249738	ENST00000764992.1	n.380+2428A>G		intron_variant	Intron 2 of 4
ENSG00000249738	ENST00000765003.1	n.387+2428A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15444 AN: 152162 Hom.: 838 Cov.: 32

Gnomad AFR AF: 0.0851

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.0404

Gnomad SAS AF: 0.0642

Gnomad FIN AF: 0.0712

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.101 AC: 15456 AN: 152282 Hom.: 842 Cov.: 32 AF XY: 0.0988 AC XY: 7355 AN XY: 74454

African (AFR) AF: 0.0850 AC: 3532 AN: 41558

American (AMR) AF: 0.139 AC: 2134 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 637 AN: 3472

East Asian (EAS) AF: 0.0405 AC: 210 AN: 5190

South Asian (SAS) AF: 0.0640 AC: 309 AN: 4826

European-Finnish (FIN) AF: 0.0712 AC: 755 AN: 10600

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7486 AN: 68014

Other (OTH) AF: 0.118 AC: 249 AN: 2114

Alfa AF: 0.113 Hom.: 3230

Bravo AF: 0.109

Asia WGS AF: 0.0610 AC: 211 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.43
DANN	Benign	0.22
PhyloP100		-0.54

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3181224; hg19: chr5-158740850;