chr2-194682669-G-A

Variant names:

• chr2-194682669-G-A
• rs801350

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 0.944 in 152,132 control chromosomes in the GnomAD database, including 67,773 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 0.94 (67773 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• 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: 0.944 AC: 143460 AN: 152016 Hom.: 67738 Cov.: 30

Gnomad AFR AF: 0.911

Gnomad AMI AF: 0.881

Gnomad AMR AF: 0.962

Gnomad ASJ AF: 0.953

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.973

Gnomad FIN AF: 0.973

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.949

Gnomad OTH AF: 0.937

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

GnomAD4 genome AF: 0.944 AC: 143549 AN: 152132 Hom.: 67773 Cov.: 30 AF XY: 0.946 AC XY: 70354 AN XY: 74362

African (AFR) AF: 0.910 AC: 37785 AN: 41500

American (AMR) AF: 0.962 AC: 14681 AN: 15256

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

East Asian (EAS) AF: 1.00 AC: 5154 AN: 5156

South Asian (SAS) AF: 0.972 AC: 4684 AN: 4818

European-Finnish (FIN) AF: 0.973 AC: 10320 AN: 10602

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

European-Non Finnish (NFE) AF: 0.949 AC: 64559 AN: 68018

Other (OTH) AF: 0.937 AC: 1974 AN: 2106

Alfa AF: 0.948 Hom.: 115174

Bravo AF: 0.941

Asia WGS AF: 0.977 AC: 3399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.76
DANN	Benign	0.66
PhyloP100		-0.028

Splicing

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

Other links and lift over

dbSNP: rs801350; hg19: chr2-195547393;