2-60232671-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 0.477 in 151,714 control chromosomes in the GnomAD database, including 17,407 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 0.48 (17407 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.346

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.501 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: 0.477 AC: 72264 AN: 151596 Hom.: 17400 Cov.: 32

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.477 AC: 72310 AN: 151714 Hom.: 17407 Cov.: 32 AF XY: 0.472 AC XY: 34968 AN XY: 74154

Gnomad4 AFR AF: 0.441

Gnomad4 AMR AF: 0.500

Gnomad4 ASJ AF: 0.486

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.498

Alfa AF: 0.403 Hom.: 1595

Bravo AF: 0.484

Asia WGS AF: 0.355 AC: 1226 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	3.1
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs359268; hg19: chr2-60459806;