rs1374486

Variant names:

• chr1-159610613-G-A
• rs1374486

Your query was ambiguous. Multiple possible variants found:

• chr1-159610613-G-A
• chr1-159610613-G-C
• chr1-159610613-G-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 0.259 in 151,958 control chromosomes in the GnomAD database, including 6,021 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 0.26 (6021 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.733
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.785 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: 0.259 AC: 39298 AN: 151840 Hom.: 6010 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.806

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.259 AC: 39344 AN: 151958 Hom.: 6021 Cov.: 32 AF XY: 0.267 AC XY: 19825 AN XY: 74242

African (AFR) AF: 0.256 AC: 10623 AN: 41416

American (AMR) AF: 0.305 AC: 4654 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 677 AN: 3466

East Asian (EAS) AF: 0.805 AC: 4152 AN: 5156

South Asian (SAS) AF: 0.220 AC: 1064 AN: 4830

European-Finnish (FIN) AF: 0.312 AC: 3286 AN: 10544

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14114 AN: 67966

Other (OTH) AF: 0.236 AC: 497 AN: 2108

Alfa AF: 0.241 Hom.: 2909

Bravo AF: 0.261

Asia WGS AF: 0.505 AC: 1752 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.21
DANN	Benign	0.28
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs1374486; hg19: chr1-159580403;