6-30237630-G-T

Variant names:

• chr6-30237630-G-T
• rs2844779
• ENST00000453558.2:n.663-3180C>A

Variant summary

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

The NR_052012.1(HCG17):​n.410-3180C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 151,822 control chromosomes in the GnomAD database, including 7,080 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 0.30 (7080 hom., cov: 30)
• Consequence: HCG17 NR_052012.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.768
• Publications: 27 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=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.332 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCG17	NR_052012.1		n.410-3180C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCG18	ENST00000453558.2	TSL:5	n.663-3180C>A		intron	N/A
	HCG18	ENST00000844410.1		n.317-3180C>A		intron	N/A
	HCG18	ENST00000844411.1		n.361-3180C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.303 AC: 46016 AN: 151704 Hom.: 7070 Cov.: 30

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.303 AC: 46058 AN: 151822 Hom.: 7080 Cov.: 30 AF XY: 0.303 AC XY: 22439 AN XY: 74166

African (AFR) AF: 0.310 AC: 12825 AN: 41400

American (AMR) AF: 0.339 AC: 5180 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 919 AN: 3464

East Asian (EAS) AF: 0.286 AC: 1475 AN: 5166

South Asian (SAS) AF: 0.194 AC: 936 AN: 4824

European-Finnish (FIN) AF: 0.311 AC: 3255 AN: 10470

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.302 AC: 20489 AN: 67918

Other (OTH) AF: 0.283 AC: 597 AN: 2112

Alfa AF: 0.297 Hom.: 14897

Bravo AF: 0.309

Asia WGS AF: 0.221 AC: 768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.4
DANN	Benign	0.82
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs2844779; hg19: chr6-30205407;