6-61285855-C-T

Variant names:

• chr6-61285855-C-T
• rs2342002

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.335 AC: 13892 AN: 41412

American (AMR) AF: 0.186 AC: 2822 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 509 AN: 3458

East Asian (EAS) AF: 0.0504 AC: 256 AN: 5078

South Asian (SAS) AF: 0.101 AC: 487 AN: 4818

European-Finnish (FIN) AF: 0.134 AC: 1416 AN: 10592

Middle Eastern (MID) AF: 0.123 AC: 36 AN: 292

European-Non Finnish (NFE) AF: 0.211 AC: 14311 AN: 67808

Other (OTH) AF: 0.198 AC: 417 AN: 2108

Alfa AF: 0.205 Hom.: 1580

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

Other links and lift over

dbSNP: rs2342002; hg19: chr6-61951860;