rs2840381

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;