6-153683836-T-C

Variant names:

• chr6-153683836-T-C
• rs2186141

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 0.499 in 152,040 control chromosomes in the GnomAD database, including 19,384 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 (19384 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.606 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: 0.499 AC: 75793 AN: 151922 Hom.: 19354 Cov.: 32

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.592

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: 0.499 AC: 75863 AN: 152040 Hom.: 19384 Cov.: 32 AF XY: 0.501 AC XY: 37230 AN XY: 74318

African (AFR) AF: 0.553 AC: 22928 AN: 41470

American (AMR) AF: 0.617 AC: 9426 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1882 AN: 3464

East Asian (EAS) AF: 0.583 AC: 3002 AN: 5152

South Asian (SAS) AF: 0.570 AC: 2752 AN: 4824

European-Finnish (FIN) AF: 0.444 AC: 4700 AN: 10576

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

European-Non Finnish (NFE) AF: 0.432 AC: 29386 AN: 67956

Other (OTH) AF: 0.529 AC: 1117 AN: 2112

Alfa AF: 0.459 Hom.: 2108

Bravo AF: 0.521

Asia WGS AF: 0.585 AC: 2035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.54
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2186141; hg19: chr6-154004971;