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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.957 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

Gnomad4 AFR AF: 0.958

Gnomad4 AMR AF: 0.966

Gnomad4 ASJ AF: 0.953

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.972

Gnomad4 FIN AF: 0.973

Gnomad4 NFE AF: 0.949

Gnomad4 OTH AF: 0.948

Alfa AF: 0.951 Hom.: 30589

Bravo AF: 0.956

Asia WGS AF: 0.982 AC: 3413 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs801378; hg19: chr2-195559997;