rs2517527

Positions:

• chr6-31053770-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.83+239A>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 0.654 in 151,946 control chromosomes in the GnomAD database, including 32,800 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 0.65 (32800 hom., cov: 31)
• Consequence: HCG22 NR_003948.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.856

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HCG22	NR_003948.3	n.83+239A>G		intron_variant, non_coding_transcript_variant
HCG22	NR_145427.2	n.83+239A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HCG22	ENST00000565192.1	n.82+239A>G		intron_variant, non_coding_transcript_variant		2
HCG22	ENST00000562344.1	n.32+239A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99331 AN: 151828 Hom.: 32766 Cov.: 31

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.840

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.764

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.654 AC: 99402 AN: 151946 Hom.: 32800 Cov.: 31 AF XY: 0.652 AC XY: 48423 AN XY: 74274

Gnomad4 AFR AF: 0.721

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.840

Gnomad4 EAS AF: 0.659

Gnomad4 SAS AF: 0.714

Gnomad4 FIN AF: 0.606

Gnomad4 NFE AF: 0.619

Gnomad4 OTH AF: 0.681

Alfa AF: 0.635 Hom.: 21274

Bravo AF: 0.656

Asia WGS AF: 0.685 AC: 2386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.2
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2517527; hg19: chr6-31021547;