chr2-36060309-C-T

Variant names:

• chr2-36060309-C-T
• rs2666128

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 0.466 in 151,738 control chromosomes in the GnomAD database, including 18,234 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 0.47 (18234 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.69 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: 0.466 AC: 70591 AN: 151620 Hom.: 18197 Cov.: 31

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.466 AC: 70691 AN: 151738 Hom.: 18234 Cov.: 31 AF XY: 0.468 AC XY: 34717 AN XY: 74142

Gnomad4 AFR AF: 0.657

Gnomad4 AMR AF: 0.518

Gnomad4 ASJ AF: 0.295

Gnomad4 EAS AF: 0.709

Gnomad4 SAS AF: 0.513

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.426

Alfa AF: 0.388 Hom.: 5097

Bravo AF: 0.487

Asia WGS AF: 0.602 AC: 2087 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.36
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2666128; hg19: chr2-36287452;