Genetic Variant ENST00000744989.1:n.48+2642A>T (chr13-37599679-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000744989.1(ENSG00000297050):n.48+2642A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,076 control chromosomes in the GnomAD database, including 3,711 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 0.20 ( 3711 hom., cov: 32)

Consequence

ENSG00000297050
ENST00000744989.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0140

Publications

9 publications found

Variant links:

Genes affected

ENSG00000297050 (HGNC:):

ENSG00000297050 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=-0.81).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.272 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
ENSG00000297050	ENST00000744989.1 link	n.48+2642A>T		intron_variant	Intron 1 of 4
ENSG00000297050	ENST00000744990.1 link	n.70+2642A>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes

AF:

0.201

AC:

30527

AN:

151958

Hom.:

3712

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0781

Gnomad AMI

AF:

0.305

Gnomad AMR

AF:

0.170

Gnomad ASJ

AF:

0.212

Gnomad EAS

AF:

0.0633

Gnomad SAS

AF:

0.136

Gnomad FIN

AF:

0.334

Gnomad MID

AF:

0.201

Gnomad NFE

AF:

0.275

Gnomad OTH

AF:

0.202

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

GnomAD4 genome

AF:

0.201

AC:

30529

AN:

152076

Hom.:

3711

Cov.:

AF XY:

0.201

AC XY:

14920

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.0779

AC:

3236

AN:

41554

American (AMR)

AF:

0.170

AC:

2592

AN:

15246

Ashkenazi Jewish (ASJ)

AF:

0.212

AC:

737

AN:

3472

East Asian (EAS)

AF:

0.0637

AC:

330

AN:

5182

South Asian (SAS)

AF:

0.136

AC:

655

AN:

4824

European-Finnish (FIN)

AF:

0.334

AC:

3527

AN:

10574

Middle Eastern (MID)

AF:

0.202

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.275

AC:

18686

AN:

67910

Other (OTH)

AF:

0.203

AC:

429

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1197

2395

3592

4790

5987

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

334

668

1002

1336

1670

<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:

0.141

Hom.:

288

Bravo

AF:

0.183

Asia WGS

AF:

0.144

AC:

503

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

1.7

(source)

DANN

Benign

0.78

PhyloP100

0.014

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