rs17164371

Variant names:

• chr7-128735318-C-T
• rs17164371

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 0.111 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0576 AC: 2395 AN: 41554

American (AMR) AF: 0.251 AC: 3834 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0513 AC: 178 AN: 3472

East Asian (EAS) AF: 0.577 AC: 2969 AN: 5146

South Asian (SAS) AF: 0.184 AC: 888 AN: 4830

European-Finnish (FIN) AF: 0.106 AC: 1117 AN: 10578

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0760 AC: 5170 AN: 68018

Other (OTH) AF: 0.103 AC: 217 AN: 2112

Alfa AF: 0.0997 Hom.: 811

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
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs17164371; hg19: chr7-128375372;