6-31057031-A-G

Variant names:

• chr6-31057031-A-G
• rs9262632
• ENST00000426185.2:n.1559+121A>G

Variant summary

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

The ENST00000426185.2(HCG22):​n.1559+121A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0637 in 152,534 control chromosomes in the GnomAD database, including 398 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 0.064 (394 hom., cov: 32)
  • Exomes 𝑓: 0.097 (4 hom.)
• Consequence: HCG22 ENST00000426185.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 39 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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.114 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+121A>G		intron	N/A
	HCG22	NR_145427.2		n.1193+121A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCG22	ENST00000426185.2	TSL:2	n.1559+121A>G		intron	N/A
	HCG22	ENST00000562344.2	TSL:5	n.1287+121A>G		intron	N/A
	HCG22	ENST00000565192.1	TSL:2	n.1192+121A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0636 AC: 9684 AN: 152168 Hom.: 393 Cov.: 32

Gnomad AFR AF: 0.0428

Gnomad AMI AF: 0.0363

Gnomad AMR AF: 0.0797

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.0565

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0531

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0610

Gnomad OTH AF: 0.0900

GnomAD4 exome AF: 0.0968 AC: 24 AN: 248 Hom.: 4 AF XY: 0.0759 AC XY: 12 AN XY: 158

African (AFR) AF: 0.00 AC: 0 AN: 8

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.0500 AC: 1 AN: 20

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.125 AC: 22 AN: 176

Other (OTH) AF: 0.0278 AC: 1 AN: 36

GnomAD4 genome AF: 0.0636 AC: 9685 AN: 152286 Hom.: 394 Cov.: 32 AF XY: 0.0653 AC XY: 4865 AN XY: 74456

African (AFR) AF: 0.0429 AC: 1784 AN: 41572

American (AMR) AF: 0.0796 AC: 1217 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 836 AN: 3468

East Asian (EAS) AF: 0.0567 AC: 294 AN: 5188

South Asian (SAS) AF: 0.122 AC: 587 AN: 4824

European-Finnish (FIN) AF: 0.0531 AC: 563 AN: 10610

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0610 AC: 4150 AN: 68016

Other (OTH) AF: 0.0905 AC: 191 AN: 2110

Alfa AF: 0.0663 Hom.: 1582

Bravo AF: 0.0639

Asia WGS AF: 0.120 AC: 416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.21
DANN	Benign	0.27
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs9262632; hg19: chr6-31024808;