10-71856818-C-T

Variant names:

• chr10-71856818-C-T
• rs4746097

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 0.308 in 152,126 control chromosomes in the GnomAD database, including 7,673 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 0.31 (7673 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.49
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46837 AN: 152008 Hom.: 7658 Cov.: 32

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.308 AC: 46889 AN: 152126 Hom.: 7673 Cov.: 32 AF XY: 0.311 AC XY: 23142 AN XY: 74380

African (AFR) AF: 0.416 AC: 17243 AN: 41486

American (AMR) AF: 0.302 AC: 4619 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 934 AN: 3472

East Asian (EAS) AF: 0.382 AC: 1976 AN: 5172

South Asian (SAS) AF: 0.333 AC: 1605 AN: 4824

European-Finnish (FIN) AF: 0.338 AC: 3576 AN: 10576

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16178 AN: 68002

Other (OTH) AF: 0.285 AC: 600 AN: 2108

Alfa AF: 0.265 Hom.: 19528

Bravo AF: 0.313

Asia WGS AF: 0.331 AC: 1154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.078
DANN	Benign	0.82
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs4746097; hg19: chr10-73616575;