rs3116636

Positions:

• chr1-159716693-G-A

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 0.251 in 150,436 control chromosomes in the GnomAD database, including 5,408 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 0.25 (5408 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220

Genes affected

(HGNC:):

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 = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.159716693G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.251 AC: 37751 AN: 150364 Hom.: 5407 Cov.: 30

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.0602

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.251 AC: 37775 AN: 150436 Hom.: 5408 Cov.: 30 AF XY: 0.253 AC XY: 18525 AN XY: 73318

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.0602

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.261

Alfa AF: 0.306 Hom.: 6804

Bravo AF: 0.244

Asia WGS AF: 0.163 AC: 567 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	3.2
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3116636; hg19: chr1-159686483;