10-49227831-T-C

Variant names:

• chr10-49227831-T-C
• rs7912808

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 0.954 in 152,310 control chromosomes in the GnomAD database, including 69,615 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 0.95 (69615 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.642
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.987 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: 0.954 AC: 145228 AN: 152192 Hom.: 69585 Cov.: 33

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.975

Gnomad AMR AF: 0.981

Gnomad ASJ AF: 0.982

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.987

Gnomad FIN AF: 0.996

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.994

Gnomad OTH AF: 0.970

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

GnomAD4 genome AF: 0.954 AC: 145315 AN: 152310 Hom.: 69615 Cov.: 33 AF XY: 0.956 AC XY: 71193 AN XY: 74484

African (AFR) AF: 0.856 AC: 35542 AN: 41540

American (AMR) AF: 0.981 AC: 15013 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.982 AC: 3408 AN: 3472

East Asian (EAS) AF: 0.997 AC: 5170 AN: 5186

South Asian (SAS) AF: 0.987 AC: 4763 AN: 4824

European-Finnish (FIN) AF: 0.996 AC: 10582 AN: 10622

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.994 AC: 67612 AN: 68038

Other (OTH) AF: 0.970 AC: 2051 AN: 2114

Alfa AF: 0.975 Hom.: 15061

Bravo AF: 0.947

Asia WGS AF: 0.967 AC: 3361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.3
DANN	Benign	0.76
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs7912808; hg19: chr10-50435876;