6-31478132-A-G

Variant names:

• chr6-31478132-A-G
• rs2395488
• ENST00000666495.2:n.1201A>G

Variant summary

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

The ENST00000666495.2(HCP5):​n.1201A>G 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 0.339 in 151,452 control chromosomes in the GnomAD database, including 9,115 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 0.34 (9115 hom., cov: 31)
• Consequence: HCP5 ENST00000666495.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.653
• Publications: 37 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000666495.2. 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	ENST00000666495.2		n.1201A>G		non_coding_transcript_exon	Exon 2 of 2
	HCP5	ENST00000718213.1		n.96-12530A>G		intron	N/A
	HCP5	ENST00000718214.1		n.96-12530A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51290 AN: 151336 Hom.: 9105 Cov.: 31

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.339 AC: 51324 AN: 151452 Hom.: 9115 Cov.: 31 AF XY: 0.337 AC XY: 24978 AN XY: 74018

African (AFR) AF: 0.301 AC: 12412 AN: 41168

American (AMR) AF: 0.349 AC: 5296 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1345 AN: 3460

East Asian (EAS) AF: 0.591 AC: 3027 AN: 5120

South Asian (SAS) AF: 0.358 AC: 1718 AN: 4798

European-Finnish (FIN) AF: 0.308 AC: 3258 AN: 10562

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.341 AC: 23171 AN: 67868

Other (OTH) AF: 0.324 AC: 680 AN: 2096

Alfa AF: 0.357 Hom.: 27187

Bravo AF: 0.343

Asia WGS AF: 0.472 AC: 1639 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.6
DANN	Benign	0.76
PhyloP100		0.65

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: rs2395488;

hg19: chr6-31445909;