6-29833697-T-C

Variant names:

• chr6-29833697-T-C
• rs2517892

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 0.387 in 151,938 control chromosomes in the GnomAD database, including 12,366 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 0.39 (12366 hom., cov: 32)
• Consequence: HCGVIII-2 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29
• Publications: 17 publications found

Genes affected

HCGVIII-2 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.524 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: 0.387 AC: 58706 AN: 151820 Hom.: 12339 Cov.: 32

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.387 AC: 58786 AN: 151938 Hom.: 12366 Cov.: 32 AF XY: 0.389 AC XY: 28866 AN XY: 74260

African (AFR) AF: 0.530 AC: 21933 AN: 41376

American (AMR) AF: 0.462 AC: 7053 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1290 AN: 3468

East Asian (EAS) AF: 0.513 AC: 2654 AN: 5174

South Asian (SAS) AF: 0.505 AC: 2428 AN: 4812

European-Finnish (FIN) AF: 0.242 AC: 2552 AN: 10548

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19610 AN: 67970

Other (OTH) AF: 0.418 AC: 882 AN: 2110

Alfa AF: 0.320 Hom.: 7658

Bravo AF: 0.408

Asia WGS AF: 0.585 AC: 2029 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	3.2
DANN	Benign	0.26
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs2517892; hg19: chr6-29801474;