6-31057327-G-A

Variant names:

• chr6-31057327-G-A
• rs2523848
• ENST00000426185.2:n.1559+417G>A

Variant summary

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

The ENST00000426185.2(HCG22):​n.1559+417G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,076 control chromosomes in the GnomAD database, including 3,734 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 (3734 hom., cov: 31)
• Consequence: HCG22 ENST00000426185.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.208
• Publications: 11 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000426185.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCG22	NR_003948.3		n.1701+417G>A		intron	N/A
	HCG22	NR_145427.2		n.1193+417G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCG22	ENST00000426185.2	TSL:2	n.1559+417G>A		intron	N/A
	HCG22	ENST00000562344.2	TSL:5	n.1287+417G>A		intron	N/A
	HCG22	ENST00000565192.1	TSL:2	n.1192+417G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.211 AC: 31990 AN: 151958 Hom.: 3726 Cov.: 31

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.0890

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.211 AC: 32026 AN: 152076 Hom.: 3734 Cov.: 31 AF XY: 0.213 AC XY: 15869 AN XY: 74360

African (AFR) AF: 0.276 AC: 11437 AN: 41444

American (AMR) AF: 0.214 AC: 3268 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1517 AN: 3466

East Asian (EAS) AF: 0.281 AC: 1455 AN: 5178

South Asian (SAS) AF: 0.366 AC: 1761 AN: 4818

European-Finnish (FIN) AF: 0.135 AC: 1434 AN: 10584

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10478 AN: 67988

Other (OTH) AF: 0.245 AC: 519 AN: 2116

Alfa AF: 0.185 Hom.: 2882

Bravo AF: 0.215

Asia WGS AF: 0.339 AC: 1177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.30
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs2523848; hg19: chr6-31025104;