chr6-33109999-C-T

Variant names:

• chr6-33109999-C-T
• rs6457713

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 0.149 in 140,830 control chromosomes in the GnomAD database, including 2,656 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 0.15 (2656 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.73
• Publications: 22 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 (AFR) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.149 AC: 20960 AN: 140740 Hom.: 2651 Cov.: 31

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.0429

Gnomad AMR AF: 0.0790

Gnomad ASJ AF: 0.0377

Gnomad EAS AF: 0.0352

Gnomad SAS AF: 0.0743

Gnomad FIN AF: 0.0579

Gnomad MID AF: 0.0169

Gnomad NFE AF: 0.0670

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.149 AC: 20983 AN: 140830 Hom.: 2656 Cov.: 31 AF XY: 0.144 AC XY: 9907 AN XY: 68722

African (AFR) AF: 0.360 AC: 14124 AN: 39242

American (AMR) AF: 0.0789 AC: 1132 AN: 14356

Ashkenazi Jewish (ASJ) AF: 0.0377 AC: 125 AN: 3312

East Asian (EAS) AF: 0.0348 AC: 65 AN: 1866

South Asian (SAS) AF: 0.0738 AC: 345 AN: 4672

European-Finnish (FIN) AF: 0.0579 AC: 581 AN: 10028

Middle Eastern (MID) AF: 0.0181 AC: 5 AN: 276

European-Non Finnish (NFE) AF: 0.0670 AC: 4305 AN: 64278

Other (OTH) AF: 0.137 AC: 263 AN: 1914

Alfa AF: 0.118 Hom.: 4175

Bravo AF: 0.147

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.36
PhyloP100		-3.7

Splicing

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

Other links and lift over

dbSNP: rs6457713; hg19: chr6-33077776;