chr2-21063185-T-C

Position:

• chr2-21063185-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 0.733 in 152,080 control chromosomes in the GnomAD database, including 42,268 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 0.73 (42268 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388

ACMG classification

Verdict is Benign. Variant got -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 = 0.884 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: 0.733 AC: 111442 AN: 151962 Hom.: 42257 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.907

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.860

Gnomad FIN AF: 0.810

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.733 AC: 111492 AN: 152080 Hom.: 42268 Cov.: 32 AF XY: 0.738 AC XY: 54864 AN XY: 74354

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.791

Gnomad4 ASJ AF: 0.674

Gnomad4 EAS AF: 0.905

Gnomad4 SAS AF: 0.860

Gnomad4 FIN AF: 0.810

Gnomad4 NFE AF: 0.815

Gnomad4 OTH AF: 0.736

Alfa AF: 0.802 Hom.: 63213

Bravo AF: 0.719

Asia WGS AF: 0.872 AC: 3032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.8
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs515135; hg19: chr2-21286057;