rs1401327

Variant names:

• chr2-49820345-G-A
• rs1401327

Your query was ambiguous. Multiple possible variants found:

• chr2-49820345-G-A
• chr2-49820345-G-C
• chr2-49820345-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 0.117 in 151,540 control chromosomes in the GnomAD database, including 1,214 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 0.12 (1214 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.316
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17804 AN: 151422 Hom.: 1213 Cov.: 32

Gnomad AFR AF: 0.0809

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0687

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.117 AC: 17802 AN: 151540 Hom.: 1214 Cov.: 32 AF XY: 0.115 AC XY: 8498 AN XY: 74018

African (AFR) AF: 0.0808 AC: 3348 AN: 41436

American (AMR) AF: 0.113 AC: 1711 AN: 15104

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 553 AN: 3464

East Asian (EAS) AF: 0.00 AC: 0 AN: 5146

South Asian (SAS) AF: 0.0679 AC: 325 AN: 4786

European-Finnish (FIN) AF: 0.124 AC: 1295 AN: 10470

Middle Eastern (MID) AF: 0.137 AC: 40 AN: 292

European-Non Finnish (NFE) AF: 0.150 AC: 10153 AN: 67840

Other (OTH) AF: 0.125 AC: 262 AN: 2092

Alfa AF: 0.136 Hom.: 2048

Bravo AF: 0.113

Asia WGS AF: 0.0390 AC: 138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.28
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs1401327; hg19: chr2-50047483;