rs17883952

Variant names:

• chr7-95348368-C-T
• rs17883952

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 0.0958 in 152,146 control chromosomes in the GnomAD database, including 1,148 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 0.096 (1148 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0958 AC: 14559 AN: 152028 Hom.: 1146 Cov.: 31

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.0209

Gnomad AMR AF: 0.0721

Gnomad ASJ AF: 0.0648

Gnomad EAS AF: 0.0276

Gnomad SAS AF: 0.0213

Gnomad FIN AF: 0.0236

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0507

Gnomad OTH AF: 0.0855

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

GnomAD4 genome AF: 0.0958 AC: 14572 AN: 152146 Hom.: 1148 Cov.: 31 AF XY: 0.0908 AC XY: 6756 AN XY: 74402

African (AFR) AF: 0.219 AC: 9089 AN: 41442

American (AMR) AF: 0.0719 AC: 1100 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0648 AC: 225 AN: 3472

East Asian (EAS) AF: 0.0277 AC: 143 AN: 5160

South Asian (SAS) AF: 0.0216 AC: 104 AN: 4822

European-Finnish (FIN) AF: 0.0236 AC: 250 AN: 10614

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0507 AC: 3447 AN: 68016

Other (OTH) AF: 0.0841 AC: 178 AN: 2116

Alfa AF: 0.0720 Hom.: 123

Bravo AF: 0.105

Asia WGS AF: 0.0360 AC: 126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.28
PhyloP100		0.30
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: rs17883952; hg19: chr7-94977680;