rs17171480

Variant names:

• chr7-35546059-G-A
• rs17171480

Your query was ambiguous. Multiple possible variants found:

• chr7-35546059-G-A
• chr7-35546059-G-T

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 0.135 in 152,088 control chromosomes in the GnomAD database, including 1,557 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 0.14 (1557 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.983
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 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: 0.135 AC: 20544 AN: 151970 Hom.: 1547 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0956

Gnomad ASJ AF: 0.0927

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.0759

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.135 AC: 20592 AN: 152088 Hom.: 1557 Cov.: 32 AF XY: 0.135 AC XY: 10027 AN XY: 74352

African (AFR) AF: 0.203 AC: 8431 AN: 41464

American (AMR) AF: 0.0955 AC: 1460 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0927 AC: 321 AN: 3462

East Asian (EAS) AF: 0.170 AC: 882 AN: 5174

South Asian (SAS) AF: 0.0760 AC: 366 AN: 4818

European-Finnish (FIN) AF: 0.138 AC: 1461 AN: 10586

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7348 AN: 67974

Other (OTH) AF: 0.134 AC: 284 AN: 2112

Alfa AF: 0.112 Hom.: 1842

Bravo AF: 0.136

Asia WGS AF: 0.135 AC: 472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.7
DANN	Benign	0.51
PhyloP100		0.98

Splicing

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

Other links and lift over

dbSNP: rs17171480; hg19: chr7-35585669;