rs213551

Variant names:

• chr2-233836743-A-G
• rs213551
• NM_018410.5:c.*834T>C

Variant summary

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

The NM_018410.5(HJURP):​c.*834T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,082 control chromosomes in the GnomAD database, including 8,609 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 0.32 (8609 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: HJURP NM_018410.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.259
• Publications: 6 publications found

Genes affected

HJURP (HGNC:25444): (Holliday junction recognition protein) Enables histone binding activity and identical protein binding activity. Involved in several processes, including CENP-A containing chromatin assembly; regulation of DNA binding activity; and regulation of protein-containing complex assembly. Located in kinetochore; mitochondrion; and nuclear lumen. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -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 = 0.489 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HJURP	NM_018410.5	c.*834T>C		3_prime_UTR_variant	Exon 9 of 9	ENST00000411486.7	NP_060880.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HJURP	ENST00000411486.7	c.*834T>C		3_prime_UTR_variant	Exon 9 of 9	1	NM_018410.5	ENSP00000414109.1
HJURP	ENST00000433484.2	n.*300+534T>C		intron_variant	Intron 2 of 2	5		ENSP00000395207.1
HJURP	ENST00000432087.5	c.*834T>C		3_prime_UTR_variant	Exon 7 of 7	2		ENSP00000407208.1
HJURP	ENST00000441687.5	c.*834T>C		3_prime_UTR_variant	Exon 6 of 6	2		ENSP00000401944.1

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48520 AN: 151964 Hom.: 8604 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.335

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.319 AC: 48543 AN: 152082 Hom.: 8609 Cov.: 32 AF XY: 0.322 AC XY: 23968 AN XY: 74336

African (AFR) AF: 0.175 AC: 7260 AN: 41514

American (AMR) AF: 0.336 AC: 5129 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1430 AN: 3464

East Asian (EAS) AF: 0.226 AC: 1168 AN: 5178

South Asian (SAS) AF: 0.506 AC: 2437 AN: 4818

European-Finnish (FIN) AF: 0.336 AC: 3549 AN: 10564

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26314 AN: 67946

Other (OTH) AF: 0.337 AC: 713 AN: 2114

Alfa AF: 0.368 Hom.: 13798

Bravo AF: 0.312

Asia WGS AF: 0.400 AC: 1392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.35
PhyloP100		-0.26
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs213551; hg19: chr2-234745389;