rs6987156

Variant names:

• chr8-56256906-T-A
• rs6987156

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 0.163 in 152,068 control chromosomes in the GnomAD database, including 2,048 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 0.16 (2048 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.202 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: 0.163 AC: 24708 AN: 151950 Hom.: 2043 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.0627

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.163 AC: 24730 AN: 152068 Hom.: 2048 Cov.: 32 AF XY: 0.161 AC XY: 11950 AN XY: 74324

African (AFR) AF: 0.205 AC: 8512 AN: 41460

American (AMR) AF: 0.167 AC: 2547 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 687 AN: 3470

East Asian (EAS) AF: 0.0625 AC: 323 AN: 5172

South Asian (SAS) AF: 0.140 AC: 674 AN: 4818

European-Finnish (FIN) AF: 0.142 AC: 1503 AN: 10570

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9928 AN: 67966

Other (OTH) AF: 0.183 AC: 387 AN: 2116

Alfa AF: 0.156 Hom.: 217

Bravo AF: 0.167

Asia WGS AF: 0.134 AC: 465 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	8.4
DANN	Benign	0.75
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs6987156; hg19: chr8-57169465;