6-27860889-C-A

Variant names:

• chr6-27860889-C-A
• rs9295751

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 0.0428 in 152,238 control chromosomes in the GnomAD database, including 341 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 0.043 (341 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830
• Publications: 3 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 (EAS) allele frequency at 95% confidence interval = 0.257 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: 0.0428 AC: 6512 AN: 152120 Hom.: 338 Cov.: 32

Gnomad AFR AF: 0.0128

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0446

Gnomad ASJ AF: 0.0363

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0835

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0334

Gnomad OTH AF: 0.0373

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

GnomAD4 genome AF: 0.0428 AC: 6521 AN: 152238 Hom.: 341 Cov.: 32 AF XY: 0.0475 AC XY: 3534 AN XY: 74422

African (AFR) AF: 0.0128 AC: 532 AN: 41538

American (AMR) AF: 0.0451 AC: 690 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0363 AC: 126 AN: 3472

East Asian (EAS) AF: 0.269 AC: 1394 AN: 5180

South Asian (SAS) AF: 0.111 AC: 537 AN: 4822

European-Finnish (FIN) AF: 0.0835 AC: 883 AN: 10578

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0334 AC: 2270 AN: 68032

Other (OTH) AF: 0.0379 AC: 80 AN: 2112

Alfa AF: 0.0330 Hom.: 212

Bravo AF: 0.0384

Asia WGS AF: 0.169 AC: 588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.86
DANN	Benign	0.47
PhyloP100		-0.083

Splicing

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

Other links and lift over

dbSNP: rs9295751; hg19: chr6-27828667;