Variant rs2255223 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_040662.1(HCP5):n.676G>A 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 0.0335 in 530,644 control chromosomes in the GnomAD database, including 566 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 ( 197 hom., cov: 32)

Exomes 𝑓: 0.031 ( 369 hom. )

Consequence

HCP5
NR_040662.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.186

Variant links:

Genes affected

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

HCP5 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HCP5	NR_040662.1 linkuse as main transcript	n.676G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HCP5	ENST00000666495.2 linkuse as main transcript	n.95+667G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.0401

AC:

6084

AN:

151796

Hom.:

197

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0378

Gnomad AMI

AF:

0.0175

Gnomad AMR

AF:

0.0630

Gnomad ASJ

AF:

0.0346

Gnomad EAS

AF:

0.00271

Gnomad SAS

AF:

0.00437

Gnomad FIN

AF:

0.00538

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0476

Gnomad OTH

AF:

0.0489

GnomAD3 exomes

AF:

0.0311

AC:

7631

AN:

245252

Hom.:

251

AF XY:

0.0302

AC XY:

4014

AN XY:

132890

show subpopulations

Gnomad AFR exome

AF:

0.0374

Gnomad AMR exome

AF:

0.0436

Gnomad ASJ exome

AF:

0.0274

Gnomad EAS exome

AF:

0.00121

Gnomad SAS exome

AF:

0.00408

Gnomad FIN exome

AF:

0.00611

Gnomad NFE exome

AF:

0.0436

Gnomad OTH exome

AF:

0.0387

GnomAD4 exome

AF:

0.0309

AC:

11708

AN:

378730

Hom.:

369

Cov.:

AF XY:

0.0287

AC XY:

6189

AN XY:

215946

show subpopulations

Gnomad4 AFR exome

AF:

0.0366

Gnomad4 AMR exome

AF:

0.0437

Gnomad4 ASJ exome

AF:

0.0286

Gnomad4 EAS exome

AF:

0.00116

Gnomad4 SAS exome

AF:

0.00426

Gnomad4 FIN exome

AF:

0.00684

Gnomad4 NFE exome

AF:

0.0442

Gnomad4 OTH exome

AF:

0.0290

GnomAD4 genome

AF:

0.0400

AC:

6084

AN:

151914

Hom.:

197

Cov.:

AF XY:

0.0377

AC XY:

2802

AN XY:

74270

show subpopulations

Gnomad4 AFR

AF:

0.0377

Gnomad4 AMR

AF:

0.0630

Gnomad4 ASJ

AF:

0.0346

Gnomad4 EAS

AF:

0.00272

Gnomad4 SAS

AF:

0.00437

Gnomad4 FIN

AF:

0.00538

Gnomad4 NFE

AF:

0.0476

Gnomad4 OTH

AF:

0.0479

Alfa

AF:

0.0415

Hom.:

136

Bravo

AF:

0.0457

Asia WGS

AF:

0.00578

AC:

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

9.8

DANN

Benign

0.59

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over