rs10485831

Variant names:

• chr20-24036939-G-A
• rs10485831
• ENST00000846737.1:n.229-10660G>A

Your query was ambiguous. Multiple possible variants found:

• chr20-24036939-G-A
• chr20-24036939-G-T

Variant summary

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

The ENST00000846737.1(ENSG00000310043):​n.229-10660G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.019 in 152,262 control chromosomes in the GnomAD database, including 50 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 0.019 (50 hom., cov: 33)
• Consequence: ENSG00000310043 ENST00000846737.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.361
• Publications: 0 publications found

Genes affected

ENSG00000310043 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0593 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310043	ENST00000846737.1	n.229-10660G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0188 AC: 2867 AN: 152144 Hom.: 46 Cov.: 33

Gnomad AFR AF: 0.0408

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.00975

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.0416

Gnomad SAS AF: 0.0652

Gnomad FIN AF: 0.00179

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.00523

Gnomad OTH AF: 0.0191

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

GnomAD4 genome AF: 0.0190 AC: 2887 AN: 152262 Hom.: 50 Cov.: 33 AF XY: 0.0199 AC XY: 1479 AN XY: 74454

African (AFR) AF: 0.0409 AC: 1698 AN: 41536

American (AMR) AF: 0.00974 AC: 149 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.000576 AC: 2 AN: 3472

East Asian (EAS) AF: 0.0413 AC: 214 AN: 5176

South Asian (SAS) AF: 0.0653 AC: 315 AN: 4826

European-Finnish (FIN) AF: 0.00179 AC: 19 AN: 10616

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.00523 AC: 356 AN: 68018

Other (OTH) AF: 0.0255 AC: 54 AN: 2114

Alfa AF: 0.0105 Hom.: 2

Bravo AF: 0.0201

Asia WGS AF: 0.0700 AC: 243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.57
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs10485831; hg19: chr20-24017576;