rs953160

Variant names:

• chr7-54069495-T-C
• rs953160

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 0.188 in 152,134 control chromosomes in the GnomAD database, including 3,116 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 0.19 (3116 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.233 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: 0.188 AC: 28517 AN: 152016 Hom.: 3112 Cov.: 32

Gnomad AFR AF: 0.0969

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0583

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.188 AC: 28543 AN: 152134 Hom.: 3116 Cov.: 32 AF XY: 0.192 AC XY: 14303 AN XY: 74362

African (AFR) AF: 0.0970 AC: 4025 AN: 41490

American (AMR) AF: 0.180 AC: 2748 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 516 AN: 3470

East Asian (EAS) AF: 0.0584 AC: 303 AN: 5184

South Asian (SAS) AF: 0.211 AC: 1018 AN: 4820

European-Finnish (FIN) AF: 0.302 AC: 3191 AN: 10578

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16081 AN: 67986

Other (OTH) AF: 0.158 AC: 334 AN: 2110

Alfa AF: 0.197 Hom.: 1233

Bravo AF: 0.173

Asia WGS AF: 0.131 AC: 458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.0
DANN	Benign	0.73
PhyloP100		0.059

Splicing

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

Other links and lift over

dbSNP: rs953160; hg19: chr7-54137188;