rs3130907

Variant names:

• chr6-31464036-A-G
• rs3130907
• ENST00000541196.3:n.198-17A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-31464036-A-G
• chr6-31464036-A-T

Variant summary

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

The ENST00000541196.3(HCP5):​n.198-17A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0834 in 446,478 control chromosomes in the GnomAD database, including 2,199 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 0.076 (611 hom., cov: 32)
  • Exomes 𝑓: 0.087 (1588 hom.)
• Consequence: HCP5 ENST00000541196.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201
• Publications: 17 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HCP5	NR_040662.1	n.766A>G		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HCP5	ENST00000541196.3	n.198-17A>G		intron_variant	Intron 2 of 3	1
HCP5	ENST00000414046.3	n.776A>G		non_coding_transcript_exon_variant	Exon 2 of 2	4
HCP5	ENST00000670109.1	n.739A>G		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0761 AC: 11539 AN: 151714 Hom.: 610 Cov.: 32

Gnomad AFR AF: 0.0371

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.0374

Gnomad ASJ AF: 0.0440

Gnomad EAS AF: 0.00523

Gnomad SAS AF: 0.0616

Gnomad FIN AF: 0.0783

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.0570

GnomAD2 exomes AF: 0.0778 AC: 14363 AN: 184570 AF XY: 0.0805

Gnomad AFR exome AF: 0.0402

Gnomad AMR exome AF: 0.0301

Gnomad ASJ exome AF: 0.0424

Gnomad EAS exome AF: 0.00218

Gnomad FIN exome AF: 0.0772

Gnomad NFE exome AF: 0.108

Gnomad OTH exome AF: 0.0712

GnomAD4 exome AF: 0.0872 AC: 25682 AN: 294646 Hom.: 1588 Cov.: 0 AF XY: 0.0883 AC XY: 14843 AN XY: 168072

African (AFR) AF: 0.0385 AC: 275 AN: 7142

American (AMR) AF: 0.0286 AC: 662 AN: 23182

Ashkenazi Jewish (ASJ) AF: 0.0436 AC: 340 AN: 7794

East Asian (EAS) AF: 0.00170 AC: 15 AN: 8798

South Asian (SAS) AF: 0.0858 AC: 4633 AN: 53994

European-Finnish (FIN) AF: 0.0818 AC: 2505 AN: 30638

Middle Eastern (MID) AF: 0.0571 AC: 147 AN: 2574

European-Non Finnish (NFE) AF: 0.109 AC: 16056 AN: 147608

Other (OTH) AF: 0.0812 AC: 1049 AN: 12916

GnomAD4 genome AF: 0.0760 AC: 11543 AN: 151832 Hom.: 611 Cov.: 32 AF XY: 0.0720 AC XY: 5340 AN XY: 74216

African (AFR) AF: 0.0371 AC: 1533 AN: 41318

American (AMR) AF: 0.0372 AC: 567 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.0440 AC: 152 AN: 3458

East Asian (EAS) AF: 0.00505 AC: 26 AN: 5150

South Asian (SAS) AF: 0.0627 AC: 302 AN: 4814

European-Finnish (FIN) AF: 0.0783 AC: 829 AN: 10584

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7870 AN: 67970

Other (OTH) AF: 0.0574 AC: 121 AN: 2108

Alfa AF: 0.0964 Hom.: 1039

Bravo AF: 0.0700

Asia WGS AF: 0.0230 AC: 82 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.1
DANN	Benign	0.32
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs3130907; hg19: chr6-31431813;