6-31210138-G-A

Variant names:

• chr6-31210138-G-A
• rs3130952
• ENST00000755328.1:n.162-46G>A

Variant summary

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

The ENST00000755328.1(HCG27):​n.162-46G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.881 in 152,096 control chromosomes in the GnomAD database, including 59,174 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 0.88 (59174 hom., cov: 31)
• Consequence: HCG27 ENST00000755328.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 33 publications found

Genes affected

HCG27 (HGNC:27366): (HLA complex group 27)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755328.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCG27	ENST00000755328.1		n.162-46G>A		intron	N/A
	HCG27	ENST00000755329.1		n.224-46G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.881 AC: 133908 AN: 151978 Hom.: 59119 Cov.: 31

Gnomad AFR AF: 0.932

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.876

Gnomad ASJ AF: 0.973

Gnomad EAS AF: 0.840

Gnomad SAS AF: 0.873

Gnomad FIN AF: 0.851

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.854

Gnomad OTH AF: 0.909

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

GnomAD4 genome AF: 0.881 AC: 134018 AN: 152096 Hom.: 59174 Cov.: 31 AF XY: 0.881 AC XY: 65531 AN XY: 74344

African (AFR) AF: 0.932 AC: 38684 AN: 41500

American (AMR) AF: 0.876 AC: 13360 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.973 AC: 3377 AN: 3472

East Asian (EAS) AF: 0.841 AC: 4350 AN: 5170

South Asian (SAS) AF: 0.872 AC: 4201 AN: 4818

European-Finnish (FIN) AF: 0.851 AC: 8996 AN: 10566

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.854 AC: 58075 AN: 68002

Other (OTH) AF: 0.907 AC: 1916 AN: 2112

Alfa AF: 0.868 Hom.: 204934

Bravo AF: 0.886

Asia WGS AF: 0.876 AC: 3048 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.7
DANN	Benign	0.73
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs3130952; hg19: chr6-31177915;