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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.118 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

Gnomad4 AFR AF: 0.0808

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0679

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.125

Alfa AF: 0.127 Hom.: 142

Bravo AF: 0.113

Asia WGS AF: 0.0390 AC: 138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
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: rs1401327; hg19: chr2-50047483;