rs3116656

Positions:

• chr1-159722582-A-G
• chr1-159722582-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 0.241 in 152,002 control chromosomes in the GnomAD database, including 5,330 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 0.24 (5330 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.44

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.31 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: 0.241 AC: 36656 AN: 151882 Hom.: 5329 Cov.: 31

Gnomad AFR AF: 0.0858

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.0612

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.241 AC: 36673 AN: 152002 Hom.: 5330 Cov.: 31 AF XY: 0.243 AC XY: 18087 AN XY: 74304

Gnomad4 AFR AF: 0.0856

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.0611

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.354

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.255

Alfa AF: 0.283 Hom.: 2424

Bravo AF: 0.233

Asia WGS AF: 0.162 AC: 564 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	11
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3116656; hg19: chr1-159692372;