6-31463980-A-G

Position:

• chr6-31463980-A-G

Variant summary

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

The NR_040662.1(HCP5):​n.710A>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 0.0907 in 527,124 control chromosomes in the GnomAD database, including 3,463 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 0.091 (942 hom., cov: 32)
  • Exomes 𝑓: 0.091 (2521 hom.)
• Consequence: HCP5 NR_040662.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HCP5	NR_040662.1	n.710A>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HCP5	ENST00000666495.2	n.95+701A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0911 AC: 13818 AN: 151730 Hom.: 941 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.00989

Gnomad AMR AF: 0.0893

Gnomad ASJ AF: 0.0753

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.0484

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.0612

Gnomad OTH AF: 0.105

GnomAD3 exomes AF: 0.0919 AC: 22287 AN: 242480 Hom.: 1655 AF XY: 0.0966 AC XY: 12706 AN XY: 131476

Gnomad AFR exome AF: 0.132

Gnomad AMR exome AF: 0.0599

Gnomad ASJ exome AF: 0.0839

Gnomad EAS exome AF: 0.194

Gnomad SAS exome AF: 0.175

Gnomad FIN exome AF: 0.0488

Gnomad NFE exome AF: 0.0656

Gnomad OTH exome AF: 0.0898

GnomAD4 exome AF: 0.0906 AC: 33996 AN: 375276 Hom.: 2521 Cov.: 0 AF XY: 0.100 AC XY: 21433 AN XY: 214230

Gnomad4 AFR exome AF: 0.135

Gnomad4 AMR exome AF: 0.0620

Gnomad4 ASJ exome AF: 0.0841

Gnomad4 EAS exome AF: 0.174

Gnomad4 SAS exome AF: 0.180

Gnomad4 FIN exome AF: 0.0480

Gnomad4 NFE exome AF: 0.0639

Gnomad4 OTH exome AF: 0.0905

GnomAD4 genome AF: 0.0911 AC: 13827 AN: 151848 Hom.: 942 Cov.: 32 AF XY: 0.0944 AC XY: 7010 AN XY: 74248

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.0892

Gnomad4 ASJ AF: 0.0753

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.0484

Gnomad4 NFE AF: 0.0612

Gnomad4 OTH AF: 0.105

Alfa AF: 0.0719 Hom.: 929

Bravo AF: 0.0926

Asia WGS AF: 0.207 AC: 717 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11752262; hg19: chr6-31431757;