6-30225736-A-G

Variant names:

• chr6-30225736-A-G
• rs3132666
• ENST00000844410.1:n.410-2091T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000844410.1(HCG18):​n.410-2091T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 152,092 control chromosomes in the GnomAD database, including 13,668 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 0.42 (13668 hom., cov: 32)
• Consequence: HCG18 ENST00000844410.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.778
• Publications: 14 publications found

Genes affected

HCG18 (HGNC:31337): (HLA complex group 18)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000844410.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCG18	ENST00000844410.1		n.410-2091T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.421 AC: 64026 AN: 151972 Hom.: 13641 Cov.: 32

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.421 AC: 64106 AN: 152092 Hom.: 13668 Cov.: 32 AF XY: 0.418 AC XY: 31064 AN XY: 74342

African (AFR) AF: 0.407 AC: 16867 AN: 41470

American (AMR) AF: 0.411 AC: 6274 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1264 AN: 3468

East Asian (EAS) AF: 0.310 AC: 1604 AN: 5170

South Asian (SAS) AF: 0.395 AC: 1903 AN: 4822

European-Finnish (FIN) AF: 0.416 AC: 4397 AN: 10582

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.447 AC: 30418 AN: 67982

Other (OTH) AF: 0.389 AC: 822 AN: 2112

Alfa AF: 0.431 Hom.: 26872

Bravo AF: 0.420

Asia WGS AF: 0.371 AC: 1290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.3
DANN	Benign	0.70
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs3132666; hg19: chr6-30193513;