rs6566339

Variant names:

• chr18-68032334-T-A
• rs6566339

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 0.0661 in 152,192 control chromosomes in the GnomAD database, including 892 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 0.066 (892 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.195 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: 0.0660 AC: 10030 AN: 152074 Hom.: 885 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0340

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.0707

Gnomad SAS AF: 0.00724

Gnomad FIN AF: 0.000847

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0106

Gnomad OTH AF: 0.0559

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

GnomAD4 genome AF: 0.0661 AC: 10066 AN: 152192 Hom.: 892 Cov.: 32 AF XY: 0.0638 AC XY: 4744 AN XY: 74410

African (AFR) AF: 0.198 AC: 8224 AN: 41502

American (AMR) AF: 0.0339 AC: 518 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0173 AC: 60 AN: 3464

East Asian (EAS) AF: 0.0709 AC: 367 AN: 5178

South Asian (SAS) AF: 0.00725 AC: 35 AN: 4828

European-Finnish (FIN) AF: 0.000847 AC: 9 AN: 10628

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0106 AC: 724 AN: 68008

Other (OTH) AF: 0.0553 AC: 117 AN: 2114

Alfa AF: 0.0457 Hom.: 74

Bravo AF: 0.0754

Asia WGS AF: 0.0330 AC: 115 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.8
DANN	Benign	0.61
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs6566339; hg19: chr18-65699571;