rs2038596

Positions:

• chr10-122354636-A-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 0.803 in 152,172 control chromosomes in the GnomAD database, including 49,482 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 0.80 (49482 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.802 AC: 122001 AN: 152052 Hom.: 49422 Cov.: 31

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.703

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.760

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.925

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.779

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

GnomAD4 genome AF: 0.803 AC: 122122 AN: 152172 Hom.: 49482 Cov.: 31 AF XY: 0.808 AC XY: 60130 AN XY: 74404

Gnomad4 AFR AF: 0.874

Gnomad4 AMR AF: 0.820

Gnomad4 ASJ AF: 0.760

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.926

Gnomad4 FIN AF: 0.773

Gnomad4 NFE AF: 0.740

Gnomad4 OTH AF: 0.782

Alfa AF: 0.769 Hom.: 5639

Bravo AF: 0.811

Asia WGS AF: 0.953 AC: 3313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.19
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2038596; hg19: chr10-124114152;