chr6-30790689-A-G

Variant names:

• chr6-30790689-A-G
• rs3131043
• ENST00000422944.1:n.352-737A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000422944.1(HCG20):​n.352-737A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 151,992 control chromosomes in the GnomAD database, including 15,598 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 0.44 (15598 hom., cov: 31)
• Consequence: HCG20 ENST00000422944.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.575
• Publications: 31 publications found

Genes affected

HCG20 (HGNC:31334): (HLA complex group 20)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000422944.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCG20	NR_138037.1		n.310-200A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCG20	ENST00000422944.1	TSL:2	n.352-737A>G		intron	N/A
	HCG20	ENST00000439406.7	TSL:2	n.342-200A>G		intron	N/A
	HCG20	ENST00000656751.1		n.268-200A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.442 AC: 67142 AN: 151874 Hom.: 15580 Cov.: 31

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.442 AC: 67207 AN: 151992 Hom.: 15598 Cov.: 31 AF XY: 0.442 AC XY: 32859 AN XY: 74304

African (AFR) AF: 0.401 AC: 16621 AN: 41444

American (AMR) AF: 0.566 AC: 8643 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2311 AN: 3462

East Asian (EAS) AF: 0.518 AC: 2675 AN: 5164

South Asian (SAS) AF: 0.670 AC: 3224 AN: 4812

European-Finnish (FIN) AF: 0.285 AC: 3018 AN: 10590

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29142 AN: 67940

Other (OTH) AF: 0.460 AC: 970 AN: 2110

Alfa AF: 0.452 Hom.: 70078

Bravo AF: 0.460

Asia WGS AF: 0.597 AC: 2080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.55
DANN	Benign	0.51
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs3131043; hg19: chr6-30758466;