Genetic Variant HLMR1:n.223-2937C>G (chr3-142930268-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000476385.1(HLMR1):n.223-2937C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 151,970 control chromosomes in the GnomAD database, including 11,199 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 0.37 ( 11199 hom., cov: 32)

Consequence

HLMR1
ENST00000476385.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.01

Publications

19 publications found

Variant links:

Genes affected

HLMR1 (HGNC:56713):

HLMR1 links:

Genome browser will be placed here

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=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HLMR1	NR_038455.1 link	n.223-2937C>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
HLMR1	ENST00000476385.1 link	n.223-2937C>G	intron_variant	Intron 1 of 4	2
HLMR1	ENST00000654729.1 link	n.131-2937C>G	intron_variant	Intron 1 of 4
HLMR1	ENST00000658594.1 link	n.196-2937C>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.368

AC:

55942

AN:

151852

Hom.:

11168

Cov.:

show subpopulations

Gnomad AFR

AF:

0.508

Gnomad AMI

AF:

0.631

Gnomad AMR

AF:

0.288

Gnomad ASJ

AF:

0.360

Gnomad EAS

AF:

0.109

Gnomad SAS

AF:

0.118

Gnomad FIN

AF:

0.327

Gnomad MID

AF:

0.291

Gnomad NFE

AF:

0.343

Gnomad OTH

AF:

0.359

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.369

AC:

56041

AN:

151970

Hom.:

11199

Cov.:

AF XY:

0.363

AC XY:

26929

AN XY:

74228

show subpopulations

African (AFR)

AF:

0.509

AC:

21078

AN:

41438

American (AMR)

AF:

0.288

AC:

4397

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.360

AC:

1249

AN:

3468

East Asian (EAS)

AF:

0.110

AC:

570

AN:

5182

South Asian (SAS)

AF:

0.119

AC:

571

AN:

4812

European-Finnish (FIN)

AF:

0.327

AC:

3442

AN:

10534

Middle Eastern (MID)

AF:

0.310

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.343

AC:

23300

AN:

67946

Other (OTH)

AF:

0.364

AC:

769

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1749

3498

5247

6996

8745

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

516

1032

1548

2064

2580

<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:

0.316

Hom.:

4179

Bravo

AF:

0.376

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.016

(source)

DANN

Benign

0.38

PhyloP100

-2.0

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over