chr6-31470817-C-T

Variant names:

• chr6-31470817-C-T
• rs2523666
• ENST00000414046.3:n.7557C>T

Variant summary

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

The ENST00000414046.3(HCP5):​n.7557C>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 0.786 in 151,716 control chromosomes in the GnomAD database, including 47,336 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 0.79 (47336 hom., cov: 31)
• Consequence: HCP5 ENST00000414046.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.201
• Publications: 7 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.881 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.7557C>T		non_coding_transcript_exon	Exon 2 of 2
	HCP5	ENST00000467369.2	TSL:4	n.218-6210C>T		intron	N/A
	HCP5	ENST00000666495.2		n.96-6210C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.786 AC: 119139 AN: 151598 Hom.: 47270 Cov.: 31

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.779

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.786 AC: 119266 AN: 151716 Hom.: 47336 Cov.: 31 AF XY: 0.786 AC XY: 58339 AN XY: 74180

African (AFR) AF: 0.857 AC: 35353 AN: 41244

American (AMR) AF: 0.826 AC: 12555 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.817 AC: 2827 AN: 3460

East Asian (EAS) AF: 0.902 AC: 4657 AN: 5162

South Asian (SAS) AF: 0.769 AC: 3689 AN: 4800

European-Finnish (FIN) AF: 0.741 AC: 7832 AN: 10566

Middle Eastern (MID) AF: 0.779 AC: 226 AN: 290

European-Non Finnish (NFE) AF: 0.731 AC: 49680 AN: 67986

Other (OTH) AF: 0.802 AC: 1683 AN: 2098

Alfa AF: 0.739 Hom.: 19855

Bravo AF: 0.799

Asia WGS AF: 0.811 AC: 2821 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.7
DANN	Benign	0.099
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs2523666; hg19: chr6-31438594;