2-194317766-G-C

Position:

• chr2-194317766-G-C

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 0.914 in 152,030 control chromosomes in the GnomAD database, including 63,687 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 0.91 (63687 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.931 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.914 AC: 138894 AN: 151912 Hom.: 63652 Cov.: 31

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.992

Gnomad AMR AF: 0.904

Gnomad ASJ AF: 0.958

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.954

Gnomad FIN AF: 0.968

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.938

Gnomad OTH AF: 0.930

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

GnomAD4 genome AF: 0.914 AC: 138975 AN: 152030 Hom.: 63687 Cov.: 31 AF XY: 0.916 AC XY: 68048 AN XY: 74322

Gnomad4 AFR AF: 0.864

Gnomad4 AMR AF: 0.903

Gnomad4 ASJ AF: 0.958

Gnomad4 EAS AF: 0.844

Gnomad4 SAS AF: 0.954

Gnomad4 FIN AF: 0.968

Gnomad4 NFE AF: 0.938

Gnomad4 OTH AF: 0.922

Alfa AF: 0.929 Hom.: 8159

Bravo AF: 0.904

Asia WGS AF: 0.871 AC: 3027 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1376702; hg19: chr2-195182490;