6-156547814-G-A

Variant names:

• chr6-156547814-G-A
• rs502281

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 0.136 in 152,168 control chromosomes in the GnomAD database, including 1,483 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 0.14 (1483 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.33
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20600 AN: 152050 Hom.: 1480 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.0787

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.136 AC: 20619 AN: 152168 Hom.: 1483 Cov.: 32 AF XY: 0.136 AC XY: 10128 AN XY: 74370

African (AFR) AF: 0.176 AC: 7304 AN: 41528

American (AMR) AF: 0.112 AC: 1711 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 384 AN: 3472

East Asian (EAS) AF: 0.146 AC: 756 AN: 5176

South Asian (SAS) AF: 0.0788 AC: 380 AN: 4822

European-Finnish (FIN) AF: 0.158 AC: 1672 AN: 10574

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7983 AN: 68006

Other (OTH) AF: 0.126 AC: 267 AN: 2116

Alfa AF: 0.125 Hom.: 2625

Bravo AF: 0.134

Asia WGS AF: 0.156 AC: 543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.5
DANN	Benign	0.57
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs502281; hg19: chr6-156868948;