rs10485831

chr20-24036939-G-Achr20-24036939-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;