6-31208558-C-T

Variant names:

• chr6-31208558-C-T
• rs3887152
• ENST00000755328.1:n.162-1626C>T

Variant summary

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

The ENST00000755328.1(HCG27):​n.162-1626C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 152,010 control chromosomes in the GnomAD database, including 9,535 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 0.35 (9535 hom., cov: 32)
• Consequence: HCG27 ENST00000755328.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167
• Publications: 23 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=-0.59).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.36 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCG27	ENST00000755328.1		n.162-1626C>T		intron	N/A
	HCG27	ENST00000755329.1		n.223+81C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53571 AN: 151892 Hom.: 9532 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.353 AC: 53592 AN: 152010 Hom.: 9535 Cov.: 32 AF XY: 0.352 AC XY: 26130 AN XY: 74292

African (AFR) AF: 0.345 AC: 14309 AN: 41470

American (AMR) AF: 0.366 AC: 5585 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1167 AN: 3470

East Asian (EAS) AF: 0.282 AC: 1460 AN: 5174

South Asian (SAS) AF: 0.266 AC: 1283 AN: 4824

European-Finnish (FIN) AF: 0.386 AC: 4062 AN: 10528

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24699 AN: 67966

Other (OTH) AF: 0.330 AC: 696 AN: 2112

Alfa AF: 0.355 Hom.: 26275

Bravo AF: 0.353

Asia WGS AF: 0.346 AC: 1200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	15
DANN	Benign	0.93
PhyloP100		0.17

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: rs3887152;

hg19: chr6-31176335;