chr6-31061396-C-A

Variant names:

• chr6-31061396-C-A
• rs9262648
• ENST00000805383.1:n.733+1597C>A

Variant summary

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

The ENST00000805383.1(HCG22):​n.733+1597C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 152,074 control chromosomes in the GnomAD database, including 3,859 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 0.22 (3859 hom., cov: 32)
• Consequence: HCG22 ENST00000805383.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.454
• Publications: 9 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000805383.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCG22	ENST00000805383.1		n.733+1597C>A		intron	N/A
	HCG22	ENST00000805384.1		n.553+1597C>A		intron	N/A
	HCG22	ENST00000805385.1		n.459+1613C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33902 AN: 151956 Hom.: 3861 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.252

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: 0.238

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

GnomAD4 genome AF: 0.223 AC: 33904 AN: 152074 Hom.: 3859 Cov.: 32 AF XY: 0.224 AC XY: 16658 AN XY: 74334

African (AFR) AF: 0.186 AC: 7733 AN: 41504

American (AMR) AF: 0.252 AC: 3846 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 702 AN: 3470

East Asian (EAS) AF: 0.191 AC: 987 AN: 5160

South Asian (SAS) AF: 0.219 AC: 1057 AN: 4822

European-Finnish (FIN) AF: 0.292 AC: 3081 AN: 10548

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

European-Non Finnish (NFE) AF: 0.230 AC: 15644 AN: 67994

Other (OTH) AF: 0.236 AC: 498 AN: 2110

Alfa AF: 0.230 Hom.: 3623

Bravo AF: 0.219

Asia WGS AF: 0.175 AC: 611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.62
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs9262648; hg19: chr6-31029173;