6-153684478-C-T

Variant names:

• chr6-153684478-C-T
• rs2186140

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 0.497 in 151,922 control chromosomes in the GnomAD database, including 19,234 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 0.50 (19234 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.606 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: 0.497 AC: 75498 AN: 151800 Hom.: 19207 Cov.: 31

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.497 AC: 75565 AN: 151922 Hom.: 19234 Cov.: 31 AF XY: 0.500 AC XY: 37093 AN XY: 74258

African (AFR) AF: 0.547 AC: 22682 AN: 41432

American (AMR) AF: 0.617 AC: 9409 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1880 AN: 3464

East Asian (EAS) AF: 0.583 AC: 3000 AN: 5146

South Asian (SAS) AF: 0.571 AC: 2745 AN: 4808

European-Finnish (FIN) AF: 0.444 AC: 4690 AN: 10554

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.432 AC: 29374 AN: 67940

Other (OTH) AF: 0.528 AC: 1116 AN: 2114

Alfa AF: 0.468 Hom.: 47034

Bravo AF: 0.519

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.14
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs2186140; hg19: chr6-154005613;