rs3116654

Variant names:

• chr1-159725971-A-G
• rs3116654

Your query was ambiguous. Multiple possible variants found:

• chr1-159725971-A-G
• chr1-159725971-A-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 0.0932 in 152,198 control chromosomes in the GnomAD database, including 847 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 0.093 (847 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.410

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.127 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: 0.0932 AC: 14174 AN: 152080 Hom.: 845 Cov.: 32

Gnomad AFR AF: 0.0224

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.0935

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.0344

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.0997

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

GnomAD4 genome AF: 0.0932 AC: 14178 AN: 152198 Hom.: 847 Cov.: 32 AF XY: 0.0941 AC XY: 7001 AN XY: 74388

Gnomad4 AFR AF: 0.0224 AC: 0.0223575 AN: 0.0223575

Gnomad4 AMR AF: 0.0934 AC: 0.0933613 AN: 0.0933613

Gnomad4 ASJ AF: 0.133 AC: 0.132776 AN: 0.132776

Gnomad4 EAS AF: 0.0343 AC: 0.0343364 AN: 0.0343364

Gnomad4 SAS AF: 0.102 AC: 0.10199 AN: 0.10199

Gnomad4 FIN AF: 0.149 AC: 0.149264 AN: 0.149264

Gnomad4 NFE AF: 0.129 AC: 0.129159 AN: 0.129159

Gnomad4 OTH AF: 0.0996 AC: 0.0996205 AN: 0.0996205

Alfa AF: 0.111 Hom.: 1702

Bravo AF: 0.0853

Asia WGS AF: 0.0600 AC: 209 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.1
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3116654; hg19: chr1-159695761;