10-111096562-C-T

Variant names:

• chr10-111096562-C-T
• rs7923122

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 0.0796 in 152,252 control chromosomes in the GnomAD database, including 646 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 0.080 (646 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.202
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.142 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: 0.0795 AC: 12100 AN: 152134 Hom.: 647 Cov.: 33

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0377

Gnomad ASJ AF: 0.0204

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0145

Gnomad FIN AF: 0.0805

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0638

Gnomad OTH AF: 0.0690

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

GnomAD4 genome AF: 0.0796 AC: 12113 AN: 152252 Hom.: 646 Cov.: 33 AF XY: 0.0769 AC XY: 5728 AN XY: 74452

African (AFR) AF: 0.145 AC: 6028 AN: 41538

American (AMR) AF: 0.0376 AC: 576 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0204 AC: 71 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5178

South Asian (SAS) AF: 0.0139 AC: 67 AN: 4822

European-Finnish (FIN) AF: 0.0805 AC: 854 AN: 10606

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0639 AC: 4344 AN: 68018

Other (OTH) AF: 0.0687 AC: 145 AN: 2110

Alfa AF: 0.0644 Hom.: 542

Bravo AF: 0.0793

Asia WGS AF: 0.0140 AC: 47 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.5
DANN	Benign	0.55
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs7923122; hg19: chr10-112856320;