rs2840381

Variant names:

• chr1-110675201-G-A
• rs2840381

Your query was ambiguous. Multiple possible variants found:

• chr1-110675201-G-A
• chr1-110675201-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 0.73 in 151,904 control chromosomes in the GnomAD database, including 40,624 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 0.73 (40624 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.767 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: 0.730 AC: 110774 AN: 151796 Hom.: 40600 Cov.: 32

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.771

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.753

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

GnomAD4 genome AF: 0.730 AC: 110842 AN: 151904 Hom.: 40624 Cov.: 32 AF XY: 0.723 AC XY: 53638 AN XY: 74238

Gnomad4 AFR AF: 0.774

Gnomad4 AMR AF: 0.692

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.619

Gnomad4 FIN AF: 0.707

Gnomad4 NFE AF: 0.738

Gnomad4 OTH AF: 0.751

Alfa AF: 0.745 Hom.: 5231

Bravo AF: 0.729

Asia WGS AF: 0.584 AC: 2025 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	5.5
DANN	Benign	0.96

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2840381; hg19: chr1-111217823;