rs7072793

Variant names:

• chr10-6064303-T-C
• rs7072793

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.561

Gnomad4 SAS AF: 0.533

Gnomad4 FIN AF: 0.544

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.419

Alfa AF: 0.416 Hom.: 27515

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7072793; hg19: chr10-6106266;