10-122363954-A-C

Variant names:

• chr10-122363954-A-C
• rs11200583

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 0.136 in 152,206 control chromosomes in the GnomAD database, including 1,603 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 0.14 (1603 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581
• Publications: 9 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 = 0.281 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: 0.136 AC: 20615 AN: 152088 Hom.: 1596 Cov.: 32

Gnomad AFR AF: 0.0874

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.136 AC: 20640 AN: 152206 Hom.: 1603 Cov.: 32 AF XY: 0.140 AC XY: 10441 AN XY: 74446

African (AFR) AF: 0.0875 AC: 3634 AN: 41536

American (AMR) AF: 0.166 AC: 2539 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 420 AN: 3472

East Asian (EAS) AF: 0.294 AC: 1516 AN: 5160

South Asian (SAS) AF: 0.234 AC: 1129 AN: 4828

European-Finnish (FIN) AF: 0.167 AC: 1776 AN: 10608

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9052 AN: 68004

Other (OTH) AF: 0.127 AC: 269 AN: 2110

Alfa AF: 0.137 Hom.: 6766

Bravo AF: 0.135

Asia WGS AF: 0.249 AC: 865 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	2.2
DANN	Benign	0.77
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs11200583; hg19: chr10-124123470;