rs2517524

chr6-31057936-C-Achr6-31057936-C-Gchr6-31057936-C-T

Variant summary

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

The NR_003948.3(HCG22):n.1701+1026C>A 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 0.572 in 151,996 control chromosomes in the GnomAD database, including 25,553 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 0.57 (25553 hom., cov: 31)
• Consequence: HCG22 NR_003948.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.832

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HCG22	NR_003948.3	n.1701+1026C>A		intron_variant, non_coding_transcript_variant
HCG22	NR_145427.2	n.1193+1026C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HCG22	ENST00000565192.1	n.1192+1026C>A		intron_variant, non_coding_transcript_variant		2
HCG22	ENST00000426185.1	n.1511+1026C>A		intron_variant, non_coding_transcript_variant		2
HCG22	ENST00000566475.1	n.300-1472C>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.572 AC: 86816 AN: 151878 Hom.: 25526 Cov.: 31

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.790

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.572 AC: 86883 AN: 151996 Hom.: 25553 Cov.: 31 AF XY: 0.576 AC XY: 42798 AN XY: 74304

Gnomad4 AFR AF: 0.671

Gnomad4 AMR AF: 0.559

Gnomad4 ASJ AF: 0.790

Gnomad4 EAS AF: 0.655

Gnomad4 SAS AF: 0.715

Gnomad4 FIN AF: 0.528

Gnomad4 NFE AF: 0.490

Gnomad4 OTH AF: 0.625

Alfa AF: 0.394 Hom.: 1226

Bravo AF: 0.576

Asia WGS AF: 0.676 AC: 2351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.3
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2517524; hg19: chr6-31025713;