chr2-194317766-G-C

Variant names:

• chr2-194317766-G-C
• rs1376702

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;