rs2342002

Positions:

• chr6-61285855-C-T

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 0.226 in 151,674 control chromosomes in the GnomAD database, including 4,313 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 0.23 (4313 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.331 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: 0.226 AC: 34327 AN: 151556 Hom.: 4314 Cov.: 33

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.0505

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.226 AC: 34342 AN: 151674 Hom.: 4313 Cov.: 33 AF XY: 0.217 AC XY: 16090 AN XY: 74076

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.0504

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.198

Alfa AF: 0.209 Hom.: 828

Bravo AF: 0.238

Asia WGS AF: 0.104 AC: 361 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.1
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2342002; hg19: chr6-61951860;