2-78866332-C-G

Variant names:

• chr2-78866332-C-G
• rs1521970

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 0.815 in 152,150 control chromosomes in the GnomAD database, including 50,934 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 0.82 (50934 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.303

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.956 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: 0.815 AC: 123949 AN: 152032 Hom.: 50882 Cov.: 33

Gnomad AFR AF: 0.892

Gnomad AMI AF: 0.800

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.978

Gnomad SAS AF: 0.878

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.815 AC: 124058 AN: 152150 Hom.: 50934 Cov.: 33 AF XY: 0.813 AC XY: 60480 AN XY: 74378

Gnomad4 AFR AF: 0.892

Gnomad4 AMR AF: 0.811

Gnomad4 ASJ AF: 0.822

Gnomad4 EAS AF: 0.978

Gnomad4 SAS AF: 0.877

Gnomad4 FIN AF: 0.723

Gnomad4 NFE AF: 0.766

Gnomad4 OTH AF: 0.835

Alfa AF: 0.738 Hom.: 2200

Bravo AF: 0.823

Asia WGS AF: 0.924 AC: 3194 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.57
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1521970; hg19: chr2-79093458;