rs9262651

Variant names:

• chr6-31061678-C-T
• rs9262651
• ENST00000805383.1:n.733+1879C>T

Variant summary

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

The ENST00000805383.1(HCG22):​n.733+1879C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,056 control chromosomes in the GnomAD database, including 4,151 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 0.23 (4151 hom., cov: 32)
• Consequence: HCG22 ENST00000805383.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 9 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.25 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.733+1879C>T		intron	N/A
	HCG22	ENST00000805384.1		n.553+1879C>T		intron	N/A
	HCG22	ENST00000805385.1		n.459+1895C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35218 AN: 151938 Hom.: 4153 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.232 AC: 35221 AN: 152056 Hom.: 4151 Cov.: 32 AF XY: 0.233 AC XY: 17282 AN XY: 74326

African (AFR) AF: 0.190 AC: 7867 AN: 41462

American (AMR) AF: 0.257 AC: 3921 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 711 AN: 3468

East Asian (EAS) AF: 0.193 AC: 1000 AN: 5178

South Asian (SAS) AF: 0.228 AC: 1098 AN: 4820

European-Finnish (FIN) AF: 0.304 AC: 3209 AN: 10548

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16531 AN: 67988

Other (OTH) AF: 0.240 AC: 508 AN: 2116

Alfa AF: 0.241 Hom.: 3837

Bravo AF: 0.227

Asia WGS AF: 0.181 AC: 631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.27
PhyloP100		-1.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9262651;

hg19: chr6-31029455;