6-32686863-G-T

Variant names:

• chr6-32686863-G-T
• rs2856688

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 0.25 in 152,078 control chromosomes in the GnomAD database, including 5,092 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 0.25 (5092 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123
• Publications: 21 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.250 AC: 38010 AN: 151960 Hom.: 5087 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.250 AC: 38044 AN: 152078 Hom.: 5092 Cov.: 32 AF XY: 0.256 AC XY: 19035 AN XY: 74336

African (AFR) AF: 0.209 AC: 8656 AN: 41480

American (AMR) AF: 0.372 AC: 5678 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1179 AN: 3472

East Asian (EAS) AF: 0.332 AC: 1715 AN: 5162

South Asian (SAS) AF: 0.344 AC: 1660 AN: 4826

European-Finnish (FIN) AF: 0.264 AC: 2782 AN: 10554

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.228 AC: 15530 AN: 67988

Other (OTH) AF: 0.266 AC: 562 AN: 2114

Alfa AF: 0.240 Hom.: 4342

Bravo AF: 0.262

Asia WGS AF: 0.282 AC: 981 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.4
DANN	Benign	0.65
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs2856688; hg19: chr6-32654640;