rs10485831

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.361

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.0409

Gnomad4 AMR AF: 0.00974

Gnomad4 ASJ AF: 0.000576

Gnomad4 EAS AF: 0.0413

Gnomad4 SAS AF: 0.0653

Gnomad4 FIN AF: 0.00179

Gnomad4 NFE AF: 0.00523

Gnomad4 OTH AF: 0.0255

Alfa AF: 0.00987 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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485831; hg19: chr20-24017576;