rs757158

Positions:

• chr7-95326216-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 0.57 in 152,078 control chromosomes in the GnomAD database, including 27,282 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 0.57 (27282 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.937

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 = 0.839 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: 0.570 AC: 86576 AN: 151960 Hom.: 27221 Cov.: 32

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.570 AC: 86702 AN: 152078 Hom.: 27282 Cov.: 32 AF XY: 0.575 AC XY: 42729 AN XY: 74344

Gnomad4 AFR AF: 0.847

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.557

Gnomad4 SAS AF: 0.570

Gnomad4 FIN AF: 0.600

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.497

Alfa AF: 0.445 Hom.: 20668

Bravo AF: 0.571

Asia WGS AF: 0.589 AC: 2046 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	0.35
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs757158; hg19: chr7-94955528;