rs17883952

Variant names:

• chr7-95348368-C-T
• rs17883952

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 0.0958 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0958 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

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.0719

Gnomad4 ASJ AF: 0.0648

Gnomad4 EAS AF: 0.0277

Gnomad4 SAS AF: 0.0216

Gnomad4 FIN AF: 0.0236

Gnomad4 NFE AF: 0.0507

Gnomad4 OTH AF: 0.0841

Alfa AF: 0.0680 Hom.: 104

Bravo AF: 0.105

Asia WGS AF: 0.0360 AC: 126 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	1.7
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17883952; hg19: chr7-94977680;