rs2377342

Positions:

• chr2-105980625-A-G

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/exons	MANE	UniProt

Ensembl

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