dbSNP rs2608077: HLMR1:n.195+2294G>A (chr3-142914604-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000658594.1(HLMR1):n.195+2294G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 151,986 control chromosomes in the GnomAD database, including 10,192 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 0.35 ( 10192 hom., cov: 32)

Consequence

HLMR1
ENST00000658594.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.302

Publications

4 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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HLMR1	ENST00000658594.1 link	n.195+2294G>A		intron_variant	Intron 1 of 2
HLMR1	ENST00000663511.1 link	n.169+2294G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.352

AC:

53518

AN:

151868

Hom.:

10180

Cov.:

show subpopulations

Gnomad AFR

AF:

0.504

Gnomad AMI

AF:

0.262

Gnomad AMR

AF:

0.359

Gnomad ASJ

AF:

0.285

Gnomad EAS

AF:

0.392

Gnomad SAS

AF:

0.325

Gnomad FIN

AF:

0.274

Gnomad MID

AF:

0.415

Gnomad NFE

AF:

0.274

Gnomad OTH

AF:

0.351

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

GnomAD4 genome

AF:

0.352

AC:

53566

AN:

151986

Hom.:

10192

Cov.:

AF XY:

0.353

AC XY:

26208

AN XY:

74292

show subpopulations

African (AFR)

AF:

0.504

AC:

20877

AN:

41418

American (AMR)

AF:

0.359

AC:

5487

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.285

AC:

988

AN:

3470

East Asian (EAS)

AF:

0.392

AC:

2023

AN:

5160

South Asian (SAS)

AF:

0.323

AC:

1553

AN:

4802

European-Finnish (FIN)

AF:

0.274

AC:

2900

AN:

10572

Middle Eastern (MID)

AF:

0.398

AC:

117

AN:

294

European-Non Finnish (NFE)

AF:

0.274

AC:

18651

AN:

67976

Other (OTH)

AF:

0.346

AC:

733

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1691

3382

5072

6763

8454

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

520

1040

1560

2080

2600

<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:

0.293

Hom.:

3115

Bravo

AF:

0.363

Asia WGS

AF:

0.357

AC:

1241

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

7.6

(source)

DANN

Benign

0.63

PhyloP100

0.30

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