chr2-194668056-A-G

Variant names:

• chr2-194668056-A-G
• rs801278

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 0.962 in 152,282 control chromosomes in the GnomAD database, including 70,446 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 (70446 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.318
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• 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: 0.962 AC: 146345 AN: 152164 Hom.: 70394 Cov.: 32

Gnomad AFR AF: 0.974

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.968

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: 0.951

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

GnomAD4 genome AF: 0.962 AC: 146455 AN: 152282 Hom.: 70446 Cov.: 32 AF XY: 0.963 AC XY: 71724 AN XY: 74452

African (AFR) AF: 0.974 AC: 40471 AN: 41560

American (AMR) AF: 0.968 AC: 14802 AN: 15290

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

East Asian (EAS) AF: 1.00 AC: 5184 AN: 5186

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

European-Finnish (FIN) AF: 0.973 AC: 10327 AN: 10610

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

European-Non Finnish (NFE) AF: 0.949 AC: 64574 AN: 68014

Other (OTH) AF: 0.951 AC: 2012 AN: 2116

Alfa AF: 0.958 Hom.: 9014

Bravo AF: 0.962

Asia WGS AF: 0.983 AC: 3412 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.45
DANN	Benign	0.47
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs801278; hg19: chr2-195532780;