6-33011832-T-C

Variant names:

• chr6-33011832-T-C
• rs4713603

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 0.513 in 152,140 control chromosomes in the GnomAD database, including 20,493 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 0.51 (20493 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.493
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.62 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: 0.513 AC: 77957 AN: 152022 Hom.: 20480 Cov.: 33

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.513 AC: 78004 AN: 152140 Hom.: 20493 Cov.: 33 AF XY: 0.516 AC XY: 38383 AN XY: 74372

African (AFR) AF: 0.627 AC: 26016 AN: 41512

American (AMR) AF: 0.444 AC: 6791 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 1968 AN: 3472

East Asian (EAS) AF: 0.505 AC: 2606 AN: 5164

South Asian (SAS) AF: 0.545 AC: 2631 AN: 4828

European-Finnish (FIN) AF: 0.533 AC: 5645 AN: 10584

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30723 AN: 67978

Other (OTH) AF: 0.523 AC: 1102 AN: 2108

Alfa AF: 0.471 Hom.: 65310

Bravo AF: 0.508

Asia WGS AF: 0.570 AC: 1982 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	13
DANN	Benign	0.81
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs4713603; hg19: chr6-32979609;