2-64800490-T-C

Position:

• chr2-64800490-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 0.225 in 152,182 control chromosomes in the GnomAD database, including 4,303 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 0.22 (4303 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.495

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.392 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: 0.225 AC: 34157 AN: 152064 Hom.: 4301 Cov.: 32

Gnomad AFR AF: 0.0990

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.225 AC: 34172 AN: 152182 Hom.: 4303 Cov.: 32 AF XY: 0.228 AC XY: 16949 AN XY: 74392

Gnomad4 AFR AF: 0.0990

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.240

Alfa AF: 0.268 Hom.: 11624

Bravo AF: 0.215

Asia WGS AF: 0.270 AC: 938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.58
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11683197; hg19: chr2-65027624;