rs7792457

Positions:

• chr7-21152762-C-A
• chr7-21152762-C-T

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 0.121 in 151,892 control chromosomes in the GnomAD database, including 1,528 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 0.12 (1528 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18390 AN: 151774 Hom.: 1526 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0808

Gnomad ASJ AF: 0.0905

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.0397

Gnomad FIN AF: 0.0414

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0821

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.121 AC: 18408 AN: 151892 Hom.: 1528 Cov.: 32 AF XY: 0.117 AC XY: 8654 AN XY: 74212

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.0808

Gnomad4 ASJ AF: 0.0905

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.0396

Gnomad4 FIN AF: 0.0414

Gnomad4 NFE AF: 0.0821

Gnomad4 OTH AF: 0.104

Alfa AF: 0.0871 Hom.: 308

Bravo AF: 0.129

Asia WGS AF: 0.0990 AC: 344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7792457; hg19: chr7-21192381;