chr5-156864594-T-C

Variant names:

• chr5-156864594-T-C
• rs6876040

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 0.101 in 152,256 control chromosomes in the GnomAD database, including 869 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 0.10 (869 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.498
• Publications: 0 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 = 0.148 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: 0.100 AC: 15262 AN: 152138 Hom.: 854 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.0882

Gnomad ASJ AF: 0.0637

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0982

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0713

Gnomad OTH AF: 0.0784

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

GnomAD4 genome AF: 0.101 AC: 15334 AN: 152256 Hom.: 869 Cov.: 32 AF XY: 0.102 AC XY: 7615 AN XY: 74460

African (AFR) AF: 0.151 AC: 6273 AN: 41526

American (AMR) AF: 0.0890 AC: 1361 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0637 AC: 221 AN: 3468

East Asian (EAS) AF: 0.110 AC: 572 AN: 5190

South Asian (SAS) AF: 0.145 AC: 697 AN: 4818

European-Finnish (FIN) AF: 0.0982 AC: 1042 AN: 10610

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0712 AC: 4847 AN: 68034

Other (OTH) AF: 0.0776 AC: 164 AN: 2114

Alfa AF: 0.0801 Hom.: 352

Bravo AF: 0.101

Asia WGS AF: 0.135 AC: 469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.0
DANN	Benign	0.31
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs6876040; hg19: chr5-156291605;