rs17751931

Variant names:

• chr3-127037647-G-A
• rs17751931

Your query was ambiguous. Multiple possible variants found:

• chr3-127037647-G-A
• chr3-127037647-G-C

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 0.115 in 152,254 control chromosomes in the GnomAD database, including 1,060 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 (1060 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.286

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.133 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: 0.115 AC: 17457 AN: 152136 Hom.: 1060 Cov.: 33

Gnomad AFR AF: 0.0999

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.00501

Gnomad SAS AF: 0.0518

Gnomad FIN AF: 0.0975

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.115 AC: 17469 AN: 152254 Hom.: 1060 Cov.: 33 AF XY: 0.112 AC XY: 8309 AN XY: 74424

Gnomad4 AFR AF: 0.0999

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.00483

Gnomad4 SAS AF: 0.0525

Gnomad4 FIN AF: 0.0975

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.132

Alfa AF: 0.130 Hom.: 632

Bravo AF: 0.117

Asia WGS AF: 0.0340 AC: 122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17751931; hg19: chr3-126756490;