6-31060568-C-T

Variant names:

• chr6-31060568-C-T
• rs2517518
• ENST00000566475.2:n.1520C>T

Variant summary

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

The ENST00000566475.2(HCG22):​n.1520C>T 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 0.208 in 152,122 control chromosomes in the GnomAD database, including 3,641 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 0.21 (3641 hom., cov: 32)
• Consequence: HCG22 ENST00000566475.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HCG22	ENST00000566475.2	n.1520C>T		non_coding_transcript_exon_variant	Exon 2 of 2	4
HCG22	ENST00000805393.1	n.1382C>T		non_coding_transcript_exon_variant	Exon 2 of 2
HCG22	ENST00000805394.1	n.1578C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31567 AN: 152004 Hom.: 3633 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.208 AC: 31604 AN: 152122 Hom.: 3641 Cov.: 32 AF XY: 0.210 AC XY: 15651 AN XY: 74366

African (AFR) AF: 0.275 AC: 11411 AN: 41488

American (AMR) AF: 0.210 AC: 3211 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1472 AN: 3470

East Asian (EAS) AF: 0.281 AC: 1451 AN: 5172

South Asian (SAS) AF: 0.362 AC: 1744 AN: 4818

European-Finnish (FIN) AF: 0.133 AC: 1409 AN: 10578

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10256 AN: 67992

Other (OTH) AF: 0.237 AC: 501 AN: 2110

Alfa AF: 0.178 Hom.: 9376

Bravo AF: 0.213

Asia WGS AF: 0.334 AC: 1162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.61
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs2517518; hg19: chr6-31028345;