rs2517527

Variant names:

• chr6-31053770-A-G
• rs2517527
• ENST00000562344.2:n.86+239A>G

Variant summary

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

The ENST00000562344.2(HCG22):​n.86+239A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 151,946 control chromosomes in the GnomAD database, including 32,800 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 0.65 (32800 hom., cov: 31)
• Consequence: HCG22 ENST00000562344.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.856
• Publications: 21 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HCG22	NR_003948.3	n.83+239A>G		intron_variant	Intron 1 of 3
HCG22	NR_145427.2	n.83+239A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HCG22	ENST00000562344.2	n.86+239A>G		intron_variant	Intron 1 of 2	5
HCG22	ENST00000565192.1	n.82+239A>G		intron_variant	Intron 1 of 3	2
HCG22	ENST00000805384.1	n.161+239A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99331 AN: 151828 Hom.: 32766 Cov.: 31

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.840

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.764

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.654 AC: 99402 AN: 151946 Hom.: 32800 Cov.: 31 AF XY: 0.652 AC XY: 48423 AN XY: 74274

African (AFR) AF: 0.721 AC: 29860 AN: 41432

American (AMR) AF: 0.592 AC: 9037 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.840 AC: 2915 AN: 3470

East Asian (EAS) AF: 0.659 AC: 3387 AN: 5140

South Asian (SAS) AF: 0.714 AC: 3437 AN: 4816

European-Finnish (FIN) AF: 0.606 AC: 6399 AN: 10564

Middle Eastern (MID) AF: 0.757 AC: 221 AN: 292

European-Non Finnish (NFE) AF: 0.619 AC: 42043 AN: 67932

Other (OTH) AF: 0.681 AC: 1440 AN: 2114

Alfa AF: 0.633 Hom.: 80515

Bravo AF: 0.656

Asia WGS AF: 0.685 AC: 2386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.2
DANN	Benign	0.44
PhyloP100		0.86

Splicing

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

Other links and lift over

dbSNP: rs2517527; hg19: chr6-31021547;