rs6987156

Variant names:

• chr8-56256906-T-A
• rs6987156

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.163 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

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.0625

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.183

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6987156; hg19: chr8-57169465;