rs17164371

Variant names:

• chr7-128735318-C-T
• rs17164371

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 0.111 in 152,206 control chromosomes in the GnomAD database, including 1,907 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 0.11 (1907 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.795

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.56 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: 0.111 AC: 16860 AN: 152088 Hom.: 1905 Cov.: 32

Gnomad AFR AF: 0.0578

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.0513

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0760

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.111 AC: 16872 AN: 152206 Hom.: 1907 Cov.: 32 AF XY: 0.118 AC XY: 8755 AN XY: 74408

Gnomad4 AFR AF: 0.0576

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.0513

Gnomad4 EAS AF: 0.577

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.0760

Gnomad4 OTH AF: 0.103

Alfa AF: 0.102 Hom.: 283

Bravo AF: 0.124

Asia WGS AF: 0.338 AC: 1174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17164371; hg19: chr7-128375372;