chr2-6059998-T-A

Position:

• chr2-6059998-T-A

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.104 in 152,190 control chromosomes in the GnomAD database, including 1,295 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 0.10 (1295 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.17

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.16).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.413 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: 0.104 AC: 15778 AN: 152072 Hom.: 1291 Cov.: 33

Gnomad AFR AF: 0.0869

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0608

Gnomad OTH AF: 0.0988

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

GnomAD4 genome AF: 0.104 AC: 15792 AN: 152190 Hom.: 1295 Cov.: 33 AF XY: 0.113 AC XY: 8429 AN XY: 74410

Gnomad4 AFR AF: 0.0868

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.428

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.0608

Gnomad4 OTH AF: 0.0969

Alfa AF: 0.0806 Hom.: 75

Bravo AF: 0.101

Asia WGS AF: 0.292 AC: 1012 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.16
CADD	Benign	20
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2882452; hg19: chr2-6200130;