chr10-113250496-T-C

Variant names:

• chr10-113250496-T-C
• rs7914029

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 0.115 in 152,066 control chromosomes in the GnomAD database, including 1,673 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 0.12 (1673 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.866
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.261 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: 0.115 AC: 17456 AN: 151944 Hom.: 1661 Cov.: 30

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.0618

Gnomad ASJ AF: 0.0752

Gnomad EAS AF: 0.0692

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0470

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0536

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.115 AC: 17507 AN: 152066 Hom.: 1673 Cov.: 30 AF XY: 0.112 AC XY: 8355 AN XY: 74332

African (AFR) AF: 0.265 AC: 10986 AN: 41456

American (AMR) AF: 0.0616 AC: 942 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0752 AC: 261 AN: 3470

East Asian (EAS) AF: 0.0691 AC: 355 AN: 5138

South Asian (SAS) AF: 0.102 AC: 491 AN: 4820

European-Finnish (FIN) AF: 0.0470 AC: 498 AN: 10594

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0536 AC: 3646 AN: 67986

Other (OTH) AF: 0.103 AC: 218 AN: 2112

Alfa AF: 0.0714 Hom.: 2803

Bravo AF: 0.121

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.1
DANN	Benign	0.72
PhyloP100		0.87

Splicing

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

Other links and lift over

dbSNP: rs7914029; hg19: chr10-115010255;