dbSNP rs1656377: MLF1-DT:n.993+469A>G (chr3-158567491-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000475981.6(MLF1-DT):n.993+469A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 151,988 control chromosomes in the GnomAD database, including 28,632 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 0.61 ( 28632 hom., cov: 32)

Consequence

MLF1-DT
ENST00000475981.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.162

Publications

13 publications found

Variant links:

Genes affected

MLF1-DT (HGNC:55620): (MLF1 divergent transcript)

MLF1-DT 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MLF1-DT	NR_104147.1 link	n.993+469A>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MLF1-DT	ENST00000475981.6 link	n.993+469A>G	intron_variant	Intron 2 of 4	2
MLF1-DT	ENST00000479233.1 link	n.288+469A>G	intron_variant	Intron 3 of 3	2
MLF1-DT	ENST00000662951.1 link	n.441+469A>G	intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.608

AC:

92267

AN:

151870

Hom.:

28598

Cov.:

show subpopulations

Gnomad AFR

AF:

0.712

Gnomad AMI

AF:

0.410

Gnomad AMR

AF:

0.564

Gnomad ASJ

AF:

0.532

Gnomad EAS

AF:

0.341

Gnomad SAS

AF:

0.666

Gnomad FIN

AF:

0.562

Gnomad MID

AF:

0.652

Gnomad NFE

AF:

0.584

Gnomad OTH

AF:

0.581

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

GnomAD4 genome

AF:

0.608

AC:

92352

AN:

151988

Hom.:

28632

Cov.:

AF XY:

0.606

AC XY:

45020

AN XY:

74292

show subpopulations

African (AFR)

AF:

0.712

AC:

29538

AN:

41460

American (AMR)

AF:

0.564

AC:

8606

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.532

AC:

1842

AN:

3460

East Asian (EAS)

AF:

0.340

AC:

1757

AN:

5162

South Asian (SAS)

AF:

0.665

AC:

3207

AN:

4820

European-Finnish (FIN)

AF:

0.562

AC:

5940

AN:

10570

Middle Eastern (MID)

AF:

0.639

AC:

188

AN:

294

European-Non Finnish (NFE)

AF:

0.584

AC:

39666

AN:

67936

Other (OTH)

AF:

0.585

AC:

1234

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1841

3683

5524

7366

9207

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

762

1524

2286

3048

3810

<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:

0.588

Hom.:

44764

Bravo

AF:

0.608

Asia WGS

AF:

0.565

AC:

1963

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.91

(source)

DANN

Benign

0.49

PhyloP100

-0.16

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