dbSNP rs10519040: ENSG00000300769:n.111+2751T>C (chr15-45951939-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 ENST00000773915.1(ENSG00000300769):n.111+2751T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,058 control chromosomes in the GnomAD database, including 9,903 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 0.33 ( 9903 hom., cov: 33)

Consequence

ENSG00000300769
ENST00000773915.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.345

Publications

1 publications found

Variant links:

Genes affected

ENSG00000300769 (HGNC:):

ENSG00000300769 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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.559 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
ENSG00000300769	ENST00000773915.1 link	n.111+2751T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.325

AC:

49355

AN:

151940

Hom.:

9871

Cov.:

show subpopulations

Gnomad AFR

AF:

0.565

Gnomad AMI

AF:

0.226

Gnomad AMR

AF:

0.217

Gnomad ASJ

AF:

0.254

Gnomad EAS

AF:

0.0110

Gnomad SAS

AF:

0.163

Gnomad FIN

AF:

0.277

Gnomad MID

AF:

0.297

Gnomad NFE

AF:

0.252

Gnomad OTH

AF:

0.278

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

GnomAD4 genome

AF:

0.325

AC:

49437

AN:

152058

Hom.:

9903

Cov.:

AF XY:

0.320

AC XY:

23773

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.566

AC:

23437

AN:

41444

American (AMR)

AF:

0.217

AC:

3315

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.254

AC:

880

AN:

3464

East Asian (EAS)

AF:

0.0108

AC:

AN:

5184

South Asian (SAS)

AF:

0.164

AC:

791

AN:

4828

European-Finnish (FIN)

AF:

0.277

AC:

2932

AN:

10570

Middle Eastern (MID)

AF:

0.303

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.252

AC:

17150

AN:

67974

Other (OTH)

AF:

0.275

AC:

581

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1556

3112

4667

6223

7779

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

460

920

1380

1840

2300

<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:

0.309

Hom.:

1054

Bravo

AF:

0.329

Asia WGS

AF:

0.117

AC:

410

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

8.0

(source)

DANN

Benign

0.85

PhyloP100

-0.34

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