rs3116654

Positions:

• chr1-159725971-A-G
• chr1-159725971-A-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 0.0932 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

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AMR AF: 0.0934

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.0343

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.0996

Alfa AF: 0.0970 Hom.: 141

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;