rs17596081

Variant names:

• chr1-171777136-C-A
• rs17596081

Your query was ambiguous. Multiple possible variants found:

• chr1-171777136-C-A
• chr1-171777136-C-T

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 0.141 in 152,192 control chromosomes in the GnomAD database, including 1,868 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 (1868 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.618

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.194 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: 0.141 AC: 21429 AN: 152074 Hom.: 1868 Cov.: 32

Gnomad AFR AF: 0.0458

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.0986

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.141 AC: 21417 AN: 152192 Hom.: 1868 Cov.: 32 AF XY: 0.139 AC XY: 10370 AN XY: 74388

Gnomad4 AFR AF: 0.0456

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.0988

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.139

Alfa AF: 0.172 Hom.: 330

Bravo AF: 0.132

Asia WGS AF: 0.117 AC: 409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.8
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17596081; hg19: chr1-171746276;