rs2758886

Variant names:

• chr6-39283061-G-A
• rs2758886

Your query was ambiguous. Multiple possible variants found:

• chr6-39283061-G-A
• chr6-39283061-G-C

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 0.232 in 151,894 control chromosomes in the GnomAD database, including 4,567 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 (4567 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.854
• Publications: 34 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 (NFE) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35185 AN: 151778 Hom.: 4564 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.00620

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.232 AC: 35200 AN: 151894 Hom.: 4567 Cov.: 32 AF XY: 0.226 AC XY: 16760 AN XY: 74248

African (AFR) AF: 0.165 AC: 6824 AN: 41394

American (AMR) AF: 0.235 AC: 3589 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 833 AN: 3468

East Asian (EAS) AF: 0.00622 AC: 32 AN: 5148

South Asian (SAS) AF: 0.122 AC: 585 AN: 4808

European-Finnish (FIN) AF: 0.228 AC: 2401 AN: 10550

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20035 AN: 67960

Other (OTH) AF: 0.242 AC: 510 AN: 2104

Alfa AF: 0.241 Hom.: 3305

Bravo AF: 0.231

Asia WGS AF: 0.0630 AC: 220 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	0.14
DANN	Benign	0.48
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs2758886; hg19: chr6-39250837;