rs2377342

Variant names:

• chr2-105980625-A-G
• rs2377342

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 0.805 in 151,586 control chromosomes in the GnomAD database, including 49,380 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 0.81 (49380 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.881

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.844 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: 0.805 AC: 121978 AN: 151468 Hom.: 49324 Cov.: 29

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.841

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.805 AC: 122091 AN: 151586 Hom.: 49380 Cov.: 29 AF XY: 0.803 AC XY: 59468 AN XY: 74042

Gnomad4 AFR AF: 0.744

Gnomad4 AMR AF: 0.724

Gnomad4 ASJ AF: 0.875

Gnomad4 EAS AF: 0.766

Gnomad4 SAS AF: 0.852

Gnomad4 FIN AF: 0.841

Gnomad4 NFE AF: 0.850

Gnomad4 OTH AF: 0.809

Alfa AF: 0.819 Hom.: 7714

Bravo AF: 0.792

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.2
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2377342; hg19: chr2-106597081;