6-151473569-T-C

Variant names:

• chr6-151473569-T-C
• rs6937816

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 0.39 in 152,026 control chromosomes in the GnomAD database, including 12,726 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 0.39 (12726 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59273 AN: 151908 Hom.: 12715 Cov.: 31

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.390 AC: 59338 AN: 152026 Hom.: 12726 Cov.: 31 AF XY: 0.391 AC XY: 29066 AN XY: 74304

African (AFR) AF: 0.578 AC: 23965 AN: 41440

American (AMR) AF: 0.357 AC: 5453 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1090 AN: 3470

East Asian (EAS) AF: 0.364 AC: 1880 AN: 5170

South Asian (SAS) AF: 0.357 AC: 1719 AN: 4812

European-Finnish (FIN) AF: 0.304 AC: 3212 AN: 10566

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.306 AC: 20796 AN: 67984

Other (OTH) AF: 0.382 AC: 808 AN: 2116

Alfa AF: 0.324 Hom.: 8156

Bravo AF: 0.403

Asia WGS AF: 0.356 AC: 1237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.7
DANN	Benign	0.51
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs6937816; hg19: chr6-151794704;