6-31471286-C-T

Variant names:

• chr6-31471286-C-T
• rs2844505
• ENST00000414046.3:n.8026C>T

Variant summary

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

The ENST00000414046.3(HCP5):​n.8026C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 145,590 control chromosomes in the GnomAD database, including 45,251 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 0.78 (45251 hom., cov: 26)
• Consequence: HCP5 ENST00000414046.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 19 publications found

Genes affected

HCP5 (HGNC:21659): (HLA complex P5)

HCG26 (HGNC:29671): (HLA complex group 26)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.88 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000414046.3. 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
	HCG26	NR_002812.3		n.58C>T		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCP5	ENST00000414046.3	TSL:4	n.8026C>T		non_coding_transcript_exon	Exon 2 of 2
	HCP5	ENST00000718210.1		n.247C>T		non_coding_transcript_exon	Exon 3 of 3
	HCP5	ENST00000467369.2	TSL:4	n.218-5741C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.783 AC: 113912 AN: 145480 Hom.: 45187 Cov.: 26

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.836

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.783 AC: 114033 AN: 145590 Hom.: 45251 Cov.: 26 AF XY: 0.783 AC XY: 55709 AN XY: 71110

African (AFR) AF: 0.853 AC: 32789 AN: 38438

American (AMR) AF: 0.824 AC: 11912 AN: 14452

Ashkenazi Jewish (ASJ) AF: 0.815 AC: 2651 AN: 3254

East Asian (EAS) AF: 0.902 AC: 4503 AN: 4992

South Asian (SAS) AF: 0.765 AC: 3536 AN: 4624

European-Finnish (FIN) AF: 0.740 AC: 7591 AN: 10258

Middle Eastern (MID) AF: 0.774 AC: 212 AN: 274

European-Non Finnish (NFE) AF: 0.730 AC: 48491 AN: 66402

Other (OTH) AF: 0.799 AC: 1592 AN: 1992

Alfa AF: 0.753 Hom.: 118957

Bravo AF: 0.799

Asia WGS AF: 0.811 AC: 2819 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.38
PhyloP100		-1.5

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: rs2844505;

hg19: chr6-31439063;