rs801378

Variant names:

• chr2-194695273-A-C
• rs801378

Your query was ambiguous. Multiple possible variants found:

• chr2-194695273-A-C
• chr2-194695273-A-G
• chr2-194695273-A-T

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 0.957 in 152,032 control chromosomes in the GnomAD database, including 69,660 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 0.96 (69660 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.957 AC: 145418 AN: 151914 Hom.: 69619 Cov.: 32

Gnomad AFR AF: 0.959

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.966

Gnomad ASJ AF: 0.953

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.972

Gnomad FIN AF: 0.973

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.949

Gnomad OTH AF: 0.948

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

GnomAD4 genome AF: 0.957 AC: 145514 AN: 152032 Hom.: 69660 Cov.: 32 AF XY: 0.959 AC XY: 71240 AN XY: 74292

African (AFR) AF: 0.958 AC: 39767 AN: 41502

American (AMR) AF: 0.966 AC: 14709 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.953 AC: 3309 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5138 AN: 5140

South Asian (SAS) AF: 0.972 AC: 4693 AN: 4828

European-Finnish (FIN) AF: 0.973 AC: 10326 AN: 10610

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.949 AC: 64488 AN: 67942

Other (OTH) AF: 0.948 AC: 2001 AN: 2110

Alfa AF: 0.951 Hom.: 119249

Bravo AF: 0.956

Asia WGS AF: 0.982 AC: 3413 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.25
DANN	Benign	0.61
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs801378; hg19: chr2-195559997;