6-31062345-T-G

Variant names:

• chr6-31062345-T-G
• rs2517510
• ENST00000805383.1:n.734-1664T>G

Variant summary

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

The ENST00000805383.1(HCG22):​n.734-1664T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 151,948 control chromosomes in the GnomAD database, including 15,705 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 0.45 (15705 hom., cov: 31)
• Consequence: HCG22 ENST00000805383.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.620
• Publications: 28 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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.573 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.734-1664T>G		intron	N/A
	HCG22	ENST00000805384.1		n.554-1664T>G		intron	N/A
	HCG22	ENST00000805385.1		n.460-1664T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68336 AN: 151830 Hom.: 15689 Cov.: 31

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.450 AC: 68384 AN: 151948 Hom.: 15705 Cov.: 31 AF XY: 0.453 AC XY: 33654 AN XY: 74264

African (AFR) AF: 0.507 AC: 20993 AN: 41418

American (AMR) AF: 0.480 AC: 7318 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.643 AC: 2228 AN: 3466

East Asian (EAS) AF: 0.472 AC: 2434 AN: 5158

South Asian (SAS) AF: 0.591 AC: 2847 AN: 4814

European-Finnish (FIN) AF: 0.429 AC: 4533 AN: 10558

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26431 AN: 67962

Other (OTH) AF: 0.506 AC: 1068 AN: 2110

Alfa AF: 0.420 Hom.: 32244

Bravo AF: 0.453

Asia WGS AF: 0.522 AC: 1818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.77
DANN	Benign	0.79
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs2517510; hg19: chr6-31030122;