chr6-137640535-C-T

Variant names:

• chr6-137640535-C-T
• rs600469

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 0.536 in 151,942 control chromosomes in the GnomAD database, including 21,803 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 0.54 (21803 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.57 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: 0.535 AC: 81294 AN: 151824 Hom.: 21770 Cov.: 31

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.536 AC: 81375 AN: 151942 Hom.: 21803 Cov.: 31 AF XY: 0.532 AC XY: 39503 AN XY: 74278

African (AFR) AF: 0.576 AC: 23869 AN: 41434

American (AMR) AF: 0.563 AC: 8590 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2052 AN: 3472

East Asian (EAS) AF: 0.469 AC: 2419 AN: 5162

South Asian (SAS) AF: 0.524 AC: 2523 AN: 4812

European-Finnish (FIN) AF: 0.448 AC: 4730 AN: 10554

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35330 AN: 67930

Other (OTH) AF: 0.521 AC: 1099 AN: 2108

Alfa AF: 0.525 Hom.: 12418

Bravo AF: 0.546

Asia WGS AF: 0.486 AC: 1687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.37
DANN	Benign	0.79
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs600469; hg19: chr6-137961672;