dbSNP rs4132476: ENSG00000300201:n.344-1055C>T (chr9-118516013-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 ENST00000770012.1(ENSG00000300201):n.344-1055C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,044 control chromosomes in the GnomAD database, including 1,711 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 0.14 ( 1711 hom., cov: 32)

Consequence

ENSG00000300201
ENST00000770012.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.170

Publications

4 publications found

Variant links:

Genes affected

ENSG00000300201 (HGNC:):

ENSG00000300201 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 = 0.209 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
ENSG00000300201	ENST00000770012.1 link	n.344-1055C>T		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes

AF:

0.143

AC:

21762

AN:

151924

Hom.:

1703

Cov.:

show subpopulations

Gnomad AFR

AF:

0.213

Gnomad AMI

AF:

0.0592

Gnomad AMR

AF:

0.121

Gnomad ASJ

AF:

0.115

Gnomad EAS

AF:

0.00483

Gnomad SAS

AF:

0.0717

Gnomad FIN

AF:

0.109

Gnomad MID

AF:

0.150

Gnomad NFE

AF:

0.129

Gnomad OTH

AF:

0.147

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

GnomAD4 genome

AF:

0.143

AC:

21784

AN:

152044

Hom.:

1711

Cov.:

AF XY:

0.141

AC XY:

10461

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.213

AC:

8828

AN:

41422

American (AMR)

AF:

0.120

AC:

1837

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.115

AC:

398

AN:

3468

East Asian (EAS)

AF:

0.00484

AC:

AN:

5168

South Asian (SAS)

AF:

0.0713

AC:

344

AN:

4822

European-Finnish (FIN)

AF:

0.109

AC:

1156

AN:

10588

Middle Eastern (MID)

AF:

0.146

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.129

AC:

8793

AN:

67988

Other (OTH)

AF:

0.145

AC:

306

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

921

1843

2764

3686

4607

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

236

472

708

944

1180

<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:

0.131

Hom.:

762

Bravo

AF:

0.147

Asia WGS

AF:

0.0460

AC:

161

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

0.99

(source)

DANN

Benign

0.77

PhyloP100

-0.17

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