chr10-6064675-C-T

Variant names:

• chr10-6064675-C-T
• rs7096384

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 0.451 in 151,836 control chromosomes in the GnomAD database, including 15,839 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 0.45 (15839 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.543 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: 0.451 AC: 68472 AN: 151720 Hom.: 15811 Cov.: 31

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.451 AC: 68544 AN: 151836 Hom.: 15839 Cov.: 31 AF XY: 0.460 AC XY: 34122 AN XY: 74190

African (AFR) AF: 0.440 AC: 18191 AN: 41374

American (AMR) AF: 0.532 AC: 8124 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1057 AN: 3464

East Asian (EAS) AF: 0.560 AC: 2892 AN: 5162

South Asian (SAS) AF: 0.534 AC: 2568 AN: 4810

European-Finnish (FIN) AF: 0.547 AC: 5766 AN: 10534

Middle Eastern (MID) AF: 0.387 AC: 113 AN: 292

European-Non Finnish (NFE) AF: 0.420 AC: 28517 AN: 67922

Other (OTH) AF: 0.440 AC: 929 AN: 2110

Alfa AF: 0.300 Hom.: 766

Bravo AF: 0.448

Asia WGS AF: 0.550 AC: 1914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.28
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs7096384; hg19: chr10-6106638;