10-84032167-C-T

Variant names:

• chr10-84032167-C-T
• rs7908652

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 0.563 in 151,970 control chromosomes in the GnomAD database, including 24,234 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 0.56 (24234 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85533 AN: 151852 Hom.: 24198 Cov.: 31

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.563 AC: 85618 AN: 151970 Hom.: 24234 Cov.: 31 AF XY: 0.560 AC XY: 41596 AN XY: 74252

African (AFR) AF: 0.595 AC: 24687 AN: 41458

American (AMR) AF: 0.560 AC: 8565 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1841 AN: 3468

East Asian (EAS) AF: 0.520 AC: 2671 AN: 5138

South Asian (SAS) AF: 0.457 AC: 2197 AN: 4812

European-Finnish (FIN) AF: 0.514 AC: 5424 AN: 10548

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.563 AC: 38240 AN: 67944

Other (OTH) AF: 0.580 AC: 1223 AN: 2110

Alfa AF: 0.555 Hom.: 17001

Bravo AF: 0.571

Asia WGS AF: 0.521 AC: 1811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.81
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs7908652; hg19: chr10-85791923;