ENST00000541196.3:n.198-73A>G

Variant names:

• chr6-31463980-A-G
• rs11752262
• ENST00000541196.3:n.198-73A>G

Variant summary

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

The ENST00000541196.3(HCP5):​n.198-73A>G variant causes a intron 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 ENST00000541196.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 24 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=-0.9).
• 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 rank	MANE	Protein	UniProt
HCP5	NR_040662.1	n.710A>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.198-73A>G		intron_variant	Intron 2 of 3	1
HCP5	ENST00000414046.3	n.720A>G		non_coding_transcript_exon_variant	Exon 2 of 2	4
HCP5	ENST00000670109.1	n.683A>G		non_coding_transcript_exon_variant	Exon 2 of 2

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

GnomAD2 exomes AF: 0.0919 AC: 22287 AN: 242480 AF XY: 0.0966

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 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

African (AFR) AF: 0.135 AC: 1377 AN: 10192

American (AMR) AF: 0.0620 AC: 2118 AN: 34140

Ashkenazi Jewish (ASJ) AF: 0.0841 AC: 965 AN: 11472

East Asian (EAS) AF: 0.174 AC: 2231 AN: 12792

South Asian (SAS) AF: 0.180 AC: 11808 AN: 65778

European-Finnish (FIN) AF: 0.0480 AC: 1548 AN: 32262

Middle Eastern (MID) AF: 0.129 AC: 367 AN: 2836

European-Non Finnish (NFE) AF: 0.0639 AC: 12094 AN: 189356

Other (OTH) AF: 0.0905 AC: 1488 AN: 16448

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

African (AFR) AF: 0.130 AC: 5367 AN: 41310

American (AMR) AF: 0.0892 AC: 1358 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.0753 AC: 261 AN: 3466

East Asian (EAS) AF: 0.160 AC: 824 AN: 5144

South Asian (SAS) AF: 0.219 AC: 1053 AN: 4800

European-Finnish (FIN) AF: 0.0484 AC: 513 AN: 10604

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.0612 AC: 4159 AN: 67978

Other (OTH) AF: 0.105 AC: 222 AN: 2114

Alfa AF: 0.0725 Hom.: 2102

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs11752262; hg19: chr6-31431757; COSMIC: COSV107515454;