chr10-67868001-C-T

Variant names:

• chr10-67868001-C-T
• rs730821

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 0.744 in 151,922 control chromosomes in the GnomAD database, including 42,821 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 0.74 (42821 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.821
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.798 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: 0.744 AC: 113004 AN: 151802 Hom.: 42794 Cov.: 32

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.819

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.744 AC: 113081 AN: 151922 Hom.: 42821 Cov.: 32 AF XY: 0.735 AC XY: 54541 AN XY: 74252

African (AFR) AF: 0.742 AC: 30735 AN: 41414

American (AMR) AF: 0.715 AC: 10890 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.819 AC: 2845 AN: 3472

East Asian (EAS) AF: 0.281 AC: 1451 AN: 5168

South Asian (SAS) AF: 0.602 AC: 2902 AN: 4818

European-Finnish (FIN) AF: 0.694 AC: 7314 AN: 10534

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.803 AC: 54622 AN: 67984

Other (OTH) AF: 0.750 AC: 1580 AN: 2106

Alfa AF: 0.781 Hom.: 88136

Bravo AF: 0.740

Asia WGS AF: 0.514 AC: 1790 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.1
DANN	Benign	0.24
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs730821; hg19: chr10-69627759;