rs9262632

chr6-31057031-A-G

Variant summary

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

The NR_003948.3(HCG22):n.1701+121A>G 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 0.0637 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 NR_003948.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HCG22	NR_003948.3	n.1701+121A>G		intron_variant, non_coding_transcript_variant
HCG22	NR_145427.2	n.1193+121A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HCG22	ENST00000565192.1	n.1192+121A>G		intron_variant, non_coding_transcript_variant		2
HCG22	ENST00000426185.1	n.1511+121A>G		intron_variant, non_coding_transcript_variant		2
HCG22	ENST00000566475.1	n.300-2377A>G		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0500

Gnomad4 NFE exome AF: 0.125

Gnomad4 OTH exome AF: 0.0278

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

Gnomad4 AFR AF: 0.0429

Gnomad4 AMR AF: 0.0796

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.0567

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.0531

Gnomad4 NFE AF: 0.0610

Gnomad4 OTH AF: 0.0905

Alfa AF: 0.0723 Hom.: 711

Bravo AF: 0.0639

Asia WGS AF: 0.120 AC: 416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.21
Dann	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9262632; hg19: chr6-31024808;