rs2523840

Variant names:

• chr6-31062648-G-A
• rs2523840
• ENST00000805383.1:n.734-1361G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-31062648-G-A
• chr6-31062648-G-C
• chr6-31062648-G-T

Variant summary

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

The ENST00000805383.1(HCG22):​n.734-1361G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 151,994 control chromosomes in the GnomAD database, including 3,645 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 (3645 hom., cov: 32)
• Consequence: HCG22 ENST00000805383.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120
• Publications: 16 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.348 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.734-1361G>A		intron	N/A
	HCG22	ENST00000805384.1		n.554-1361G>A		intron	N/A
	HCG22	ENST00000805385.1		n.460-1361G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31562 AN: 151876 Hom.: 3637 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.242

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: 31598 AN: 151994 Hom.: 3645 Cov.: 32 AF XY: 0.211 AC XY: 15651 AN XY: 74284

African (AFR) AF: 0.275 AC: 11406 AN: 41444

American (AMR) AF: 0.210 AC: 3208 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1474 AN: 3468

East Asian (EAS) AF: 0.281 AC: 1454 AN: 5174

South Asian (SAS) AF: 0.362 AC: 1745 AN: 4820

European-Finnish (FIN) AF: 0.133 AC: 1400 AN: 10550

Middle Eastern (MID) AF: 0.243 AC: 71 AN: 292

European-Non Finnish (NFE) AF: 0.151 AC: 10263 AN: 67974

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

Alfa AF: 0.176 Hom.: 5299

Bravo AF: 0.213

Asia WGS AF: 0.334 AC: 1162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.61
PhyloP100		-0.012

Splicing

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

Other links and lift over

dbSNP: rs2523840; hg19: chr6-31030425;