rs757158

Variant names:

• chr7-95326216-C-T
• rs757158

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 0.57 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
• Publications: 39 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.847 AC: 35151 AN: 41520

American (AMR) AF: 0.484 AC: 7391 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1222 AN: 3468

East Asian (EAS) AF: 0.557 AC: 2870 AN: 5154

South Asian (SAS) AF: 0.570 AC: 2740 AN: 4808

European-Finnish (FIN) AF: 0.600 AC: 6337 AN: 10566

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.431 AC: 29321 AN: 67972

Other (OTH) AF: 0.497 AC: 1047 AN: 2108

Alfa AF: 0.459 Hom.: 28252

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
PhyloP100		-0.94
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs757158; hg19: chr7-94955528;