rs1003979

Positions:

• chr6-33146394-T-C
• chr6-33146394-T-G

Variant summary

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

The NR_138084.1(HCG24):​n.365-821T>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 0.565 in 151,974 control chromosomes in the GnomAD database, including 24,841 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 0.56 (24841 hom., cov: 31)
• Consequence: HCG24 NR_138084.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88

Genes affected

HCG24 (HGNC:23500): (HLA complex group 24)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.888 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HCG24	NR_138084.1	n.365-821T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HCG24	ENST00000414398.1	n.165-821T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85738 AN: 151856 Hom.: 24817 Cov.: 31

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.910

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.565 AC: 85816 AN: 151974 Hom.: 24841 Cov.: 31 AF XY: 0.573 AC XY: 42567 AN XY: 74280

Gnomad4 AFR AF: 0.478

Gnomad4 AMR AF: 0.631

Gnomad4 ASJ AF: 0.573

Gnomad4 EAS AF: 0.910

Gnomad4 SAS AF: 0.714

Gnomad4 FIN AF: 0.606

Gnomad4 NFE AF: 0.559

Gnomad4 OTH AF: 0.579

Alfa AF: 0.571 Hom.: 46849

Bravo AF: 0.564

Asia WGS AF: 0.759 AC: 2635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.35
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1003979; hg19: chr6-33114171;