rs7072793

Variant names:

• chr10-6064303-T-C
• rs7072793

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 0.417 in 152,044 control chromosomes in the GnomAD database, including 13,804 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 0.42 (13804 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.423
• Publications: 29 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.544 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: 0.416 AC: 63264 AN: 151928 Hom.: 13781 Cov.: 31

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.417 AC: 63331 AN: 152044 Hom.: 13804 Cov.: 31 AF XY: 0.426 AC XY: 31671 AN XY: 74316

African (AFR) AF: 0.319 AC: 13221 AN: 41462

American (AMR) AF: 0.521 AC: 7965 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1054 AN: 3470

East Asian (EAS) AF: 0.561 AC: 2899 AN: 5170

South Asian (SAS) AF: 0.533 AC: 2569 AN: 4816

European-Finnish (FIN) AF: 0.544 AC: 5749 AN: 10568

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28496 AN: 67966

Other (OTH) AF: 0.419 AC: 885 AN: 2112

Alfa AF: 0.414 Hom.: 41716

Bravo AF: 0.409

Asia WGS AF: 0.544 AC: 1893 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	5.0
DANN	Benign	0.27
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs7072793; hg19: chr10-6106266;