6-31464097-G-T

Position:

• chr6-31464097-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_040662.1(HCP5):​n.827G>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 0.0517 in 343,264 control chromosomes in the GnomAD database, including 758 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 0.040 (223 hom., cov: 32)
  • Exomes 𝑓: 0.061 (535 hom.)
• Consequence: HCP5 NR_040662.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0952 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HCP5	NR_040662.1	n.827G>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HCP5	ENST00000666495.2	n.95+818G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0398 AC: 6043 AN: 151886 Hom.: 225 Cov.: 32

Gnomad AFR AF: 0.00804

Gnomad AMI AF: 0.0275

Gnomad AMR AF: 0.0396

Gnomad ASJ AF: 0.0692

Gnomad EAS AF: 0.0791

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0556

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0473

Gnomad OTH AF: 0.0560

GnomAD3 exomes AF: 0.0517 AC: 6842 AN: 132220 Hom.: 282 AF XY: 0.0571 AC XY: 4025 AN XY: 70494

Gnomad AFR exome AF: 0.00700

Gnomad AMR exome AF: 0.0305

Gnomad ASJ exome AF: 0.0702

Gnomad EAS exome AF: 0.0641

Gnomad SAS exome AF: 0.113

Gnomad FIN exome AF: 0.0516

Gnomad NFE exome AF: 0.0520

Gnomad OTH exome AF: 0.0631

GnomAD4 exome AF: 0.0613 AC: 11717 AN: 191260 Hom.: 535 Cov.: 0 AF XY: 0.0696 AC XY: 7490 AN XY: 107602

Gnomad4 AFR exome AF: 0.00696

Gnomad4 AMR exome AF: 0.0290

Gnomad4 ASJ exome AF: 0.0795

Gnomad4 EAS exome AF: 0.0723

Gnomad4 SAS exome AF: 0.117

Gnomad4 FIN exome AF: 0.0520

Gnomad4 NFE exome AF: 0.0475

Gnomad4 OTH exome AF: 0.0507

GnomAD4 genome AF: 0.0397 AC: 6042 AN: 152004 Hom.: 223 Cov.: 32 AF XY: 0.0418 AC XY: 3106 AN XY: 74350

Gnomad4 AFR AF: 0.00797

Gnomad4 AMR AF: 0.0395

Gnomad4 ASJ AF: 0.0692

Gnomad4 EAS AF: 0.0795

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.0556

Gnomad4 NFE AF: 0.0473

Gnomad4 OTH AF: 0.0549

Alfa AF: 0.0447 Hom.: 168

Bravo AF: 0.0359

Asia WGS AF: 0.0640 AC: 222 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.4
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2395030; hg19: chr6-31431874;