rs2523742

chr6-30236622-C-G

Variant summary

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

The NR_052012.1(HCG17):n.410-2172G>C 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 0.104 in 152,162 control chromosomes in the GnomAD database, including 1,000 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 0.10 (1000 hom., cov: 32)
• Consequence: HCG17 NR_052012.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.176

Genes affected

HCG17 (HGNC:31339): (HLA complex group 17)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HCG17	NR_052012.1	n.410-2172G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HCG17	ENST00000453558.1	n.410-2172G>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15815 AN: 152044 Hom.: 993 Cov.: 32

Gnomad AFR AF: 0.0896

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.0643

Gnomad ASJ AF: 0.0668

Gnomad EAS AF: 0.00520

Gnomad SAS AF: 0.0588

Gnomad FIN AF: 0.0876

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.0893

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

GnomAD4 genome AF: 0.104 AC: 15851 AN: 152162 Hom.: 1000 Cov.: 32 AF XY: 0.0988 AC XY: 7349 AN XY: 74390

Gnomad4 AFR AF: 0.0898

Gnomad4 AMR AF: 0.0642

Gnomad4 ASJ AF: 0.0668

Gnomad4 EAS AF: 0.00521

Gnomad4 SAS AF: 0.0601

Gnomad4 FIN AF: 0.0876

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.0950

Alfa AF: 0.121 Hom.: 150

Bravo AF: 0.101

Asia WGS AF: 0.0520 AC: 182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
Cadd	Benign	9.3
Dann	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2523742; hg19: chr6-30204399;