rs7791070

Positions:

• chr7-17361403-T-C

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 0.315 in 152,096 control chromosomes in the GnomAD database, including 8,943 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 0.31 (8943 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.506 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: 0.314 AC: 47758 AN: 151978 Hom.: 8903 Cov.: 32

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.315 AC: 47855 AN: 152096 Hom.: 8943 Cov.: 32 AF XY: 0.313 AC XY: 23287 AN XY: 74344

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.291

Alfa AF: 0.243 Hom.: 2359

Bravo AF: 0.339

Asia WGS AF: 0.302 AC: 1051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.83
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7791070; hg19: chr7-17401027;