rs2377342

Variant names:

• chr2-105980625-A-G
• rs2377342

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.744 AC: 30729 AN: 41292

American (AMR) AF: 0.724 AC: 11041 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.875 AC: 3028 AN: 3462

East Asian (EAS) AF: 0.766 AC: 3932 AN: 5132

South Asian (SAS) AF: 0.852 AC: 4084 AN: 4792

European-Finnish (FIN) AF: 0.841 AC: 8822 AN: 10488

Middle Eastern (MID) AF: 0.856 AC: 250 AN: 292

European-Non Finnish (NFE) AF: 0.850 AC: 57705 AN: 67874

Other (OTH) AF: 0.809 AC: 1703 AN: 2104

Alfa AF: 0.857 Hom.: 10792

Bravo AF: 0.792

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.2
DANN	Benign	0.72
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs2377342; hg19: chr2-106597081;