chr10-122354636-A-T

Variant names:

• chr10-122354636-A-T
• rs2038596

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.874 AC: 36293 AN: 41504

American (AMR) AF: 0.820 AC: 12550 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.760 AC: 2640 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5158 AN: 5164

South Asian (SAS) AF: 0.926 AC: 4464 AN: 4822

European-Finnish (FIN) AF: 0.773 AC: 8192 AN: 10598

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.740 AC: 50302 AN: 67994

Other (OTH) AF: 0.782 AC: 1654 AN: 2116

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
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs2038596; hg19: chr10-124114152;