6-30769709-A-C

Variant names:

• chr6-30769709-A-C
• rs3094117
• ENST00000439406.7:n.159+2758A>C

Variant summary

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

The ENST00000439406.7(HCG20):​n.159+2758A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 151,824 control chromosomes in the GnomAD database, including 6,193 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 0.28 (6193 hom., cov: 31)
• Consequence: HCG20 ENST00000439406.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137
• Publications: 19 publications found

Genes affected

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

ENSG00000296065 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.338 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000439406.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCG20	NR_138037.1		n.127+2758A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCG20	ENST00000439406.7	TSL:2	n.159+2758A>C		intron	N/A
	HCG20	ENST00000656751.1		n.86-18982A>C		intron	N/A
	ENSG00000296065	ENST00000736000.1		n.-23T>G		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42636 AN: 151708 Hom.: 6185 Cov.: 31

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.281 AC: 42682 AN: 151824 Hom.: 6193 Cov.: 31 AF XY: 0.274 AC XY: 20347 AN XY: 74184

African (AFR) AF: 0.343 AC: 14176 AN: 41366

American (AMR) AF: 0.263 AC: 4003 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 869 AN: 3470

East Asian (EAS) AF: 0.173 AC: 890 AN: 5154

South Asian (SAS) AF: 0.309 AC: 1487 AN: 4818

European-Finnish (FIN) AF: 0.164 AC: 1728 AN: 10544

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18676 AN: 67926

Other (OTH) AF: 0.290 AC: 610 AN: 2104

Alfa AF: 0.282 Hom.: 15676

Bravo AF: 0.293

Asia WGS AF: 0.265 AC: 922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.4
DANN	Benign	0.57
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs3094117; hg19: chr6-30737486;