Genetic Variant NM_018410.5:c.*834T>C (chr2-233836743-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.259

Publications

6 publications found

Variant links:

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]

HJURP links:

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ACMG classification

Classification was made for transcript

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018410.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
HJURP	NM_018410.5	MANE Select	c.*834T>C	3_prime_UTR	Exon 9 of 9	NP_060880.3
HJURP	NM_001282962.2		c.*834T>C	3_prime_UTR	Exon 7 of 7	NP_001269891.1	Q8NCD3-2
HJURP	NM_001282963.2		c.*834T>C	3_prime_UTR	Exon 6 of 6	NP_001269892.1	Q8NCD3-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
HJURP	ENST00000411486.7	TSL:1 MANE Select	c.*834T>C	3_prime_UTR	Exon 9 of 9	ENSP00000414109.1	Q8NCD3-1
HJURP	ENST00000433484.2	TSL:5	n.*300+534T>C	intron	N/A	ENSP00000395207.1	H7C0I6
HJURP	ENST00000432087.5	TSL:2	c.*834T>C	3_prime_UTR	Exon 7 of 7	ENSP00000407208.1	Q8NCD3-2

Frequencies

GnomAD3 genomes

AF:

0.319

AC:

48520

AN:

151964

Hom.:

8604

Cov.:

show subpopulations

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:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.319

AC:

48543

AN:

152082

Hom.:

8609

Cov.:

AF XY:

0.322

AC XY:

23968

AN XY:

74336

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1649

3299

4948

6598

8247

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

504

1008

1512

2016

2520

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.3

(source)

DANN

Benign

0.35

PhyloP100

-0.26

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over