2-76482424-T-C

Position:

• chr2-76482424-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 0.132 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;