6-30772069-C-T

Variant names:

• chr6-30772069-C-T
• rs6911628
• ENST00000439406.7:n.159+5118C>T

Variant summary

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

The ENST00000439406.7(HCG20):​n.159+5118C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 151,842 control chromosomes in the GnomAD database, including 8,057 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 0.31 (8057 hom., cov: 30)
• Consequence: HCG20 ENST00000439406.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170
• Publications: 17 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.456 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCG20	NR_138037.1		n.127+5118C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCG20	ENST00000439406.7	TSL:2	n.159+5118C>T		intron	N/A
	HCG20	ENST00000656751.1		n.86-16622C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46915 AN: 151724 Hom.: 8036 Cov.: 30

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.309 AC: 46967 AN: 151842 Hom.: 8057 Cov.: 30 AF XY: 0.302 AC XY: 22385 AN XY: 74216

African (AFR) AF: 0.461 AC: 19067 AN: 41330

American (AMR) AF: 0.280 AC: 4275 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 902 AN: 3468

East Asian (EAS) AF: 0.173 AC: 893 AN: 5168

South Asian (SAS) AF: 0.234 AC: 1126 AN: 4810

European-Finnish (FIN) AF: 0.160 AC: 1692 AN: 10564

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18085 AN: 67934

Other (OTH) AF: 0.315 AC: 663 AN: 2108

Alfa AF: 0.284 Hom.: 18623

Bravo AF: 0.328

Asia WGS AF: 0.224 AC: 781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.59
PhyloP100		0.017

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6911628;

hg19: chr6-30739846;