rs1921246

Variant names:

• chr2-76482424-T-C
• rs1921246

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 0.132 in 152,138 control chromosomes in the GnomAD database, including 1,936 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 0.13 (1936 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.45 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: 0.132 AC: 20139 AN: 152020 Hom.: 1941 Cov.: 32

Gnomad AFR AF: 0.0449

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.0808

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.132 AC: 20136 AN: 152138 Hom.: 1936 Cov.: 32 AF XY: 0.134 AC XY: 9934 AN XY: 74372

Gnomad4 AFR AF: 0.0447

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.466

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.0808

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.159

Alfa AF: 0.146 Hom.: 902

Bravo AF: 0.131

Asia WGS AF: 0.339 AC: 1178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.18
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1921246; hg19: chr2-76709550;