6-31468270-T-C

Variant names:

• chr6-31468270-T-C
• rs2518028
• ENST00000414046.3:n.5010T>C

Variant summary

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

The ENST00000414046.3(HCP5):​n.5010T>C 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 0.714 in 151,670 control chromosomes in the GnomAD database, including 39,115 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 0.71 (39115 hom., cov: 31)
• Consequence: HCP5 ENST00000414046.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.746
• Publications: 22 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.866 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCP5	ENST00000414046.3	TSL:4	n.5010T>C		non_coding_transcript_exon	Exon 2 of 2
	HCP5	ENST00000467369.2	TSL:4	n.217+4762T>C		intron	N/A
	HCP5	ENST00000666495.2		n.95+4991T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.714 AC: 108217 AN: 151552 Hom.: 39084 Cov.: 31

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.795

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.719

Gnomad MID AF: 0.857

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.714 AC: 108298 AN: 151670 Hom.: 39115 Cov.: 31 AF XY: 0.721 AC XY: 53465 AN XY: 74134

African (AFR) AF: 0.724 AC: 29861 AN: 41230

American (AMR) AF: 0.795 AC: 12084 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.692 AC: 2398 AN: 3464

East Asian (EAS) AF: 0.888 AC: 4563 AN: 5140

South Asian (SAS) AF: 0.828 AC: 3990 AN: 4818

European-Finnish (FIN) AF: 0.719 AC: 7582 AN: 10546

Middle Eastern (MID) AF: 0.846 AC: 247 AN: 292

European-Non Finnish (NFE) AF: 0.668 AC: 45384 AN: 67968

Other (OTH) AF: 0.758 AC: 1597 AN: 2108

Alfa AF: 0.687 Hom.: 23354

Bravo AF: 0.722

Asia WGS AF: 0.793 AC: 2759 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.66
DANN	Benign	0.29
PhyloP100		-0.75

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: rs2518028;

hg19: chr6-31436047;