10-92450119-C-T

Variant names:

• chr10-92450119-C-T
• rs7910977

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 0.165 in 151,836 control chromosomes in the GnomAD database, including 2,324 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 0.16 (2324 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.498
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25003 AN: 151718 Hom.: 2321 Cov.: 31

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.0626

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.165 AC: 25049 AN: 151836 Hom.: 2324 Cov.: 31 AF XY: 0.167 AC XY: 12380 AN XY: 74204

African (AFR) AF: 0.227 AC: 9386 AN: 41372

American (AMR) AF: 0.222 AC: 3375 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.0626 AC: 217 AN: 3468

East Asian (EAS) AF: 0.167 AC: 862 AN: 5174

South Asian (SAS) AF: 0.188 AC: 903 AN: 4804

European-Finnish (FIN) AF: 0.133 AC: 1406 AN: 10554

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8563 AN: 67958

Other (OTH) AF: 0.136 AC: 286 AN: 2104

Alfa AF: 0.138 Hom.: 1281

Bravo AF: 0.173

Asia WGS AF: 0.170 AC: 592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	14
DANN	Benign	0.83
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs7910977; hg19: chr10-94209876;