chr10-122361043-G-A

Variant names:

• chr10-122361043-G-A
• rs984668

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 0.376 in 151,896 control chromosomes in the GnomAD database, including 11,006 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 0.38 (11006 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.459 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: 0.376 AC: 57047 AN: 151778 Hom.: 10986 Cov.: 31

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.376 AC: 57101 AN: 151896 Hom.: 11006 Cov.: 31 AF XY: 0.383 AC XY: 28423 AN XY: 74250

African (AFR) AF: 0.366 AC: 15146 AN: 41422

American (AMR) AF: 0.438 AC: 6678 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1108 AN: 3468

East Asian (EAS) AF: 0.475 AC: 2441 AN: 5138

South Asian (SAS) AF: 0.420 AC: 2018 AN: 4800

European-Finnish (FIN) AF: 0.434 AC: 4583 AN: 10550

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.354 AC: 24071 AN: 67954

Other (OTH) AF: 0.356 AC: 749 AN: 2106

Alfa AF: 0.341 Hom.: 6027

Bravo AF: 0.376

Asia WGS AF: 0.490 AC: 1704 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.12
DANN	Benign	0.65
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs984668; hg19: chr10-124120559;