chr10-111073803-T-C

Variant names:

• chr10-111073803-T-C
• rs7096359

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 0.0878 in 152,194 control chromosomes in the GnomAD database, including 641 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 0.088 (641 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.352
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.095 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0878 AC: 13346 AN: 152076 Hom.: 635 Cov.: 32

Gnomad AFR AF: 0.0707

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.0740

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.0532

Gnomad SAS AF: 0.0939

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.0969

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.0878 AC: 13367 AN: 152194 Hom.: 641 Cov.: 32 AF XY: 0.0884 AC XY: 6581 AN XY: 74414

African (AFR) AF: 0.0708 AC: 2937 AN: 41510

American (AMR) AF: 0.0739 AC: 1130 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 490 AN: 3470

East Asian (EAS) AF: 0.0529 AC: 275 AN: 5196

South Asian (SAS) AF: 0.0936 AC: 450 AN: 4808

European-Finnish (FIN) AF: 0.104 AC: 1101 AN: 10592

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.0969 AC: 6591 AN: 68004

Other (OTH) AF: 0.115 AC: 243 AN: 2112

Alfa AF: 0.0950 Hom.: 2095

Bravo AF: 0.0859

Asia WGS AF: 0.104 AC: 361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.2
DANN	Benign	0.55
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs7096359; hg19: chr10-112833561;