rs2394423

Variant names:

• chr6-31064265-G-A
• rs2394423
• ENST00000805383.1:n.990G>A

Variant summary

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

The ENST00000805383.1(HCG22):​n.990G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 152,128 control chromosomes in the GnomAD database, including 3,865 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 (3865 hom., cov: 32)
• Consequence: HCG22 ENST00000805383.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 18 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.246 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

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
	HCG22	ENST00000805383.1		n.990G>A		non_coding_transcript_exon	Exon 3 of 3
	HCG22	ENST00000805384.1		n.*73G>A		downstream_gene	N/A
	HCG22	ENST00000805385.1		n.*75G>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33932 AN: 152010 Hom.: 3867 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.223 AC: 33934 AN: 152128 Hom.: 3865 Cov.: 32 AF XY: 0.224 AC XY: 16678 AN XY: 74376

African (AFR) AF: 0.186 AC: 7728 AN: 41502

American (AMR) AF: 0.252 AC: 3855 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 702 AN: 3466

East Asian (EAS) AF: 0.191 AC: 991 AN: 5180

South Asian (SAS) AF: 0.219 AC: 1054 AN: 4818

European-Finnish (FIN) AF: 0.293 AC: 3100 AN: 10574

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.230 AC: 15647 AN: 67992

Other (OTH) AF: 0.237 AC: 501 AN: 2114

Alfa AF: 0.224 Hom.: 9642

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	-0.96
CADD	Benign	0.041
DANN	Benign	0.55
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2394423; hg19: chr6-31032042;