rs3130380

Variant names:

• chr6-30311353-G-A
• rs3130380
• ENST00000426882.6:n.797+15001C>T

Variant summary

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

The ENST00000426882.6(HCG18):​n.797+15001C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0647 in 151,420 control chromosomes in the GnomAD database, including 465 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 0.065 (465 hom., cov: 30)
• Consequence: HCG18 ENST00000426882.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

Genes affected

HCG18 (HGNC:31337): (HLA complex group 18)

HCG17 (HGNC:):

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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HCG18	NR_024052.2	n.1017+2916C>T		intron_variant	Intron 2 of 4
HCG18	NR_024053.2	n.803+15001C>T		intron_variant	Intron 1 of 3
HCG17	NR_052012.1	n.126+14656C>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HCG18	ENST00000426882.6	n.797+15001C>T		intron_variant	Intron 1 of 2	1
HCG18	ENST00000412685.9	n.508+15001C>T		intron_variant	Intron 1 of 2	2
HCG18	ENST00000413358.6	n.252+2916C>T		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.0647 AC: 9795 AN: 151302 Hom.: 465 Cov.: 30

Gnomad AFR AF: 0.0319

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.0256

Gnomad ASJ AF: 0.0303

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000417

Gnomad FIN AF: 0.0676

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0424

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

GnomAD4 genome AF: 0.0647 AC: 9794 AN: 151420 Hom.: 465 Cov.: 30 AF XY: 0.0593 AC XY: 4386 AN XY: 73968

Gnomad4 AFR AF: 0.0318

Gnomad4 AMR AF: 0.0255

Gnomad4 ASJ AF: 0.0303

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000209

Gnomad4 FIN AF: 0.0676

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.0420

Alfa AF: 0.0918 Hom.: 1381

Bravo AF: 0.0607

Asia WGS AF: 0.00404 AC: 15 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.2
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3130380; hg19: chr6-30279130;