rs2077386

Variant names:

• chr2-231931043-G-C
• rs2077386

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 0.201 in 151,944 control chromosomes in the GnomAD database, including 4,171 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 0.20 (4171 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.378 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: 0.201 AC: 30481 AN: 151826 Hom.: 4157 Cov.: 31

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.0824

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.0422

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.201 AC: 30540 AN: 151944 Hom.: 4171 Cov.: 31 AF XY: 0.199 AC XY: 14738 AN XY: 74246

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.0423

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.192

Alfa AF: 0.171 Hom.: 397

Bravo AF: 0.216

Asia WGS AF: 0.160 AC: 558 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.5
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2077386; hg19: chr2-232795753;