dbSNP rs4311994: ENSG00000305440:n.107+726C>T (chr10-111143332-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000810908.1(ENSG00000305440):n.107+726C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,252 control chromosomes in the GnomAD database, including 1,400 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 0.13 ( 1400 hom., cov: 33)

Consequence

ENSG00000305440
ENST00000810908.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.350

Publications

10 publications found

Variant links:

Genes affected

ENSG00000305440 (HGNC:):

ENSG00000305440 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 (NFE) allele frequency at 95% confidence interval = 0.149 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
ENSG00000305440	ENST00000810908.1 link	n.107+726C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.129

AC:

19585

AN:

152134

Hom.:

1400

Cov.:

show subpopulations

Gnomad AFR

AF:

0.119

Gnomad AMI

AF:

0.0855

Gnomad AMR

AF:

0.105

Gnomad ASJ

AF:

0.176

Gnomad EAS

AF:

0.00270

Gnomad SAS

AF:

0.0553

Gnomad FIN

AF:

0.138

Gnomad MID

AF:

0.190

Gnomad NFE

AF:

0.151

Gnomad OTH

AF:

0.141

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

GnomAD4 genome

AF:

0.129

AC:

19591

AN:

152252

Hom.:

1400

Cov.:

AF XY:

0.126

AC XY:

9366

AN XY:

74436

show subpopulations

African (AFR)

AF:

0.119

AC:

4932

AN:

41560

American (AMR)

AF:

0.104

AC:

1598

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.176

AC:

611

AN:

3470

East Asian (EAS)

AF:

0.00270

AC:

AN:

5182

South Asian (SAS)

AF:

0.0552

AC:

266

AN:

4820

European-Finnish (FIN)

AF:

0.138

AC:

1463

AN:

10588

Middle Eastern (MID)

AF:

0.190

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.151

AC:

10280

AN:

68012

Other (OTH)

AF:

0.139

AC:

293

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

881

1763

2644

3526

4407

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

216

432

648

864

1080

<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:

0.132

Hom.:

195

Bravo

AF:

0.125

Asia WGS

AF:

0.0470

AC:

166

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

2.2

(source)

DANN

Benign

0.76

PhyloP100

-0.35

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