chr6-31058212-C-T

Variant names:

• chr6-31058212-C-T
• rs9262638
• ENST00000426185.2:n.1560-1196C>T

Variant summary

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

The ENST00000426185.2(HCG22):​n.1560-1196C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 151,988 control chromosomes in the GnomAD database, including 3,933 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 0.23 (3933 hom., cov: 31)
• Consequence: HCG22 ENST00000426185.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200
• Publications: 16 publications found

Genes affected

HCG22 (HGNC:27780): (HLA complex group 22 (non-protein coding)) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000426185.2. 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
	HCG22	NR_003948.3		n.1702-1196C>T		intron	N/A
	HCG22	NR_145427.2		n.1194-1196C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCG22	ENST00000426185.2	TSL:2	n.1560-1196C>T		intron	N/A
	HCG22	ENST00000562344.2	TSL:5	n.1288-1196C>T		intron	N/A
	HCG22	ENST00000565192.1	TSL:2	n.1193-1196C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34344 AN: 151870 Hom.: 3935 Cov.: 31

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.226 AC: 34345 AN: 151988 Hom.: 3933 Cov.: 31 AF XY: 0.227 AC XY: 16862 AN XY: 74288

African (AFR) AF: 0.195 AC: 8083 AN: 41434

American (AMR) AF: 0.257 AC: 3928 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 702 AN: 3472

East Asian (EAS) AF: 0.191 AC: 989 AN: 5170

South Asian (SAS) AF: 0.219 AC: 1056 AN: 4814

European-Finnish (FIN) AF: 0.292 AC: 3077 AN: 10528

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15645 AN: 67986

Other (OTH) AF: 0.241 AC: 510 AN: 2114

Alfa AF: 0.227 Hom.: 11325

Bravo AF: 0.223

Asia WGS AF: 0.176 AC: 613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.9
DANN	Benign	0.84
PhyloP100		0.020

Splicing

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

Other links and lift over

dbSNP: rs9262638; hg19: chr6-31025989;