2-21063185-T-C

Variant names:

• chr2-21063185-T-C
• rs515135

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;