chr6-29833697-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HCGVIII-2		n.29833697T>C		intragenic_variant

Ensembl

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

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 v4.3

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;