rs3094654

Variant names:

• chr6-29872039-T-A
• rs3094654
• ENST00000630472.1:n.1745A>T

Your query was ambiguous. Multiple possible variants found:

• chr6-29872039-T-A
• chr6-29872039-T-C
• chr6-29872039-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000630472.1(HCP5B):​n.1745A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: HCP5B ENST00000630472.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.250
• Publications: 12 publications found

Genes affected

HCP5B (HGNC:30984): (HLA complex P5B)

ENSG00000290870 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HCP5B	NR_031762.2	n.1745A>T		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HCP5B	ENST00000630472.1	n.1745A>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000290870	ENST00000647952.1	n.2062+11515A>T		intron_variant	Intron 1 of 3
POLR1HASP	ENST00000849679.1	n.587-9213A>T		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 72142

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.1
DANN	Benign	0.32
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs3094654; hg19: chr6-29839816;