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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.805

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.236

Alfa AF: 0.231 Hom.: 1036

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1374486; hg19: chr1-159580403;