chr2-20965616-T-C

Position:

• chr2-20965616-T-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 0.784 in 152,216 control chromosomes in the GnomAD database, including 47,060 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 0.78 (47060 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.577

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.925 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.784 AC: 119190 AN: 152098 Hom.: 47018 Cov.: 33

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.811

Gnomad EAS AF: 0.947

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.822

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

GnomAD4 genome AF: 0.784 AC: 119285 AN: 152216 Hom.: 47060 Cov.: 33 AF XY: 0.784 AC XY: 58369 AN XY: 74410

Gnomad4 AFR AF: 0.853

Gnomad4 AMR AF: 0.737

Gnomad4 ASJ AF: 0.811

Gnomad4 EAS AF: 0.947

Gnomad4 SAS AF: 0.840

Gnomad4 FIN AF: 0.745

Gnomad4 NFE AF: 0.740

Gnomad4 OTH AF: 0.822

Alfa AF: 0.757 Hom.: 10327

Bravo AF: 0.788

Asia WGS AF: 0.877 AC: 3049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.92
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4665788; hg19: chr2-21188488;