rs9262639

Positions:

• chr6-31058232-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_003948.3(HCG22):​n.1702-1176C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 152,046 control chromosomes in the GnomAD database, including 3,862 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 (3862 hom., cov: 31)
• Consequence: HCG22 NR_003948.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.486

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HCG22	NR_003948.3	n.1702-1176C>T		intron_variant, non_coding_transcript_variant
HCG22	NR_145427.2	n.1194-1176C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HCG22	ENST00000565192.1	n.1193-1176C>T		intron_variant, non_coding_transcript_variant		2
HCG22	ENST00000426185.1	n.1512-1176C>T		intron_variant, non_coding_transcript_variant		2
HCG22	ENST00000566475.1	n.300-1176C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33892 AN: 151928 Hom.: 3864 Cov.: 31

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.293

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: 33894 AN: 152046 Hom.: 3862 Cov.: 31 AF XY: 0.224 AC XY: 16652 AN XY: 74312

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.236

Alfa AF: 0.233 Hom.: 4333

Bravo AF: 0.219

Asia WGS AF: 0.175 AC: 612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.6
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9262639; hg19: chr6-31026009;