6-33001680-C-T

Variant names:

• chr6-33001680-C-T
• rs172274

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 0.372 in 152,182 control chromosomes in the GnomAD database, including 10,915 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 0.37 (10915 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139
• Publications: 25 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.488 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: 0.372 AC: 56592 AN: 152064 Hom.: 10912 Cov.: 33

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.372 AC: 56644 AN: 152182 Hom.: 10915 Cov.: 33 AF XY: 0.372 AC XY: 27671 AN XY: 74426

African (AFR) AF: 0.375 AC: 15566 AN: 41500

American (AMR) AF: 0.497 AC: 7611 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1866 AN: 3472

East Asian (EAS) AF: 0.333 AC: 1727 AN: 5182

South Asian (SAS) AF: 0.466 AC: 2254 AN: 4832

European-Finnish (FIN) AF: 0.247 AC: 2614 AN: 10588

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23761 AN: 67994

Other (OTH) AF: 0.423 AC: 891 AN: 2108

Alfa AF: 0.370 Hom.: 24286

Bravo AF: 0.392

Asia WGS AF: 0.424 AC: 1474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.1
DANN	Benign	0.74
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs172274; hg19: chr6-32969457;