chr6-30243030-T-G

Variant names:

• chr6-30243030-T-G
• rs9261588
• ENST00000453558.2:n.498-719A>C

Variant summary

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

The NR_052012.1(HCG17):​n.245-719A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.918 in 152,228 control chromosomes in the GnomAD database, including 64,259 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 0.92 (64259 hom., cov: 30)
• Consequence: HCG17 NR_052012.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.394
• Publications: 22 publications found

Genes affected

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

HCG17 (HGNC:31339): (HLA complex group 17)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.96 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_052012.1. 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
	HCG17	NR_052012.1		n.245-719A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCG18	ENST00000453558.2	TSL:5	n.498-719A>C		intron	N/A
	HCG18	ENST00000844410.1		n.152-719A>C		intron	N/A
	HCG18	ENST00000844411.1		n.196-719A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.918 AC: 139566 AN: 152110 Hom.: 64194 Cov.: 30

Gnomad AFR AF: 0.968

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.934

Gnomad ASJ AF: 0.951

Gnomad EAS AF: 0.974

Gnomad SAS AF: 0.948

Gnomad FIN AF: 0.895

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.878

Gnomad OTH AF: 0.921

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

GnomAD4 genome AF: 0.918 AC: 139690 AN: 152228 Hom.: 64259 Cov.: 30 AF XY: 0.919 AC XY: 68361 AN XY: 74414

African (AFR) AF: 0.968 AC: 40213 AN: 41546

American (AMR) AF: 0.934 AC: 14284 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.951 AC: 3301 AN: 3472

East Asian (EAS) AF: 0.974 AC: 5050 AN: 5184

South Asian (SAS) AF: 0.948 AC: 4573 AN: 4822

European-Finnish (FIN) AF: 0.895 AC: 9473 AN: 10584

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.878 AC: 59715 AN: 68016

Other (OTH) AF: 0.922 AC: 1942 AN: 2106

Alfa AF: 0.901 Hom.: 123802

Bravo AF: 0.925

Asia WGS AF: 0.959 AC: 3337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	6.1
DANN	Benign	0.69
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs9261588; hg19: chr6-30210807;