2-60213064-G-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 0.388 in 151,934 control chromosomes in the GnomAD database, including 12,266 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 0.39 (12266 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.455 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: 0.388 AC: 58941 AN: 151814 Hom.: 12259 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.388 AC: 58977 AN: 151934 Hom.: 12266 Cov.: 32 AF XY: 0.391 AC XY: 28991 AN XY: 74236

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.456

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.446

Gnomad4 OTH AF: 0.415

Alfa AF: 0.262 Hom.: 652

Bravo AF: 0.391

Asia WGS AF: 0.387 AC: 1345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	5.0
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11125832; hg19: chr2-60440199;