6-151641067-C-T

Variant names:

• chr6-151641067-C-T
• rs852003

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 0.606 in 151,884 control chromosomes in the GnomAD database, including 28,719 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 0.61 (28719 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.734 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: 0.606 AC: 91965 AN: 151766 Hom.: 28686 Cov.: 30

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.606 AC: 92047 AN: 151884 Hom.: 28719 Cov.: 30 AF XY: 0.599 AC XY: 44451 AN XY: 74202

African (AFR) AF: 0.741 AC: 30717 AN: 41434

American (AMR) AF: 0.473 AC: 7220 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2191 AN: 3468

East Asian (EAS) AF: 0.420 AC: 2158 AN: 5144

South Asian (SAS) AF: 0.585 AC: 2813 AN: 4806

European-Finnish (FIN) AF: 0.514 AC: 5394 AN: 10502

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.584 AC: 39653 AN: 67952

Other (OTH) AF: 0.599 AC: 1263 AN: 2108

Alfa AF: 0.587 Hom.: 81428

Bravo AF: 0.607

Asia WGS AF: 0.553 AC: 1926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.2
DANN	Benign	0.49
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs852003; hg19: chr6-151962202;