6-30768374-C-T

Variant names:

• chr6-30768374-C-T
• rs12526186
• ENST00000439406.7:n.159+1423C>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+1423C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,120 control chromosomes in the GnomAD database, including 3,127 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 0.17 (3127 hom., cov: 31)
• Consequence: HCG20 ENST00000439406.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30
• Publications: 33 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HCG20	NR_138037.1	n.127+1423C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HCG20	ENST00000439406.7	n.159+1423C>T		intron_variant	Intron 1 of 3	2
HCG20	ENST00000656751.1	n.86-20317C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26207 AN: 152002 Hom.: 3119 Cov.: 31

Gnomad AFR AF: 0.0691

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.172 AC: 26222 AN: 152120 Hom.: 3127 Cov.: 31 AF XY: 0.178 AC XY: 13270 AN XY: 74346

African (AFR) AF: 0.0690 AC: 2866 AN: 41518

American (AMR) AF: 0.334 AC: 5106 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1396 AN: 3468

East Asian (EAS) AF: 0.370 AC: 1911 AN: 5160

South Asian (SAS) AF: 0.404 AC: 1946 AN: 4822

European-Finnish (FIN) AF: 0.114 AC: 1206 AN: 10578

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11092 AN: 67978

Other (OTH) AF: 0.201 AC: 425 AN: 2110

Alfa AF: 0.177 Hom.: 3843

Bravo AF: 0.183

Asia WGS AF: 0.369 AC: 1286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.51
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs12526186; hg19: chr6-30736151;