rs801378

Positions:

• 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/exons	MANE	UniProt

Ensembl

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