Genetic Variant ENSG00000303960:n.308+898T>G (chr7-133101533-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NR_133931.1(LOC105375512):n.148+898T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0907 in 152,194 control chromosomes in the GnomAD database, including 1,378 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 0.091 ( 1378 hom., cov: 33)

Consequence

LOC105375512
NR_133931.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.296

Publications

0 publications found

Variant links:

Genes affected

ENSG00000303960 (HGNC:):

ENSG00000303960 links:

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new If you want to explore the variant's impact on the transcript NR_133931.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.8).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_133931.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105375512	NR_133931.1		n.148+898T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303960	ENST00000798409.1		n.308+898T>G		intron	N/A
	ENSG00000303960	ENST00000798410.1		n.150+898T>G		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0905

AC:

13768

AN:

152076

Hom.:

1371

Cov.:

show subpopulations

Gnomad AFR

AF:

0.201

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.200

Gnomad ASJ

AF:

0.0444

Gnomad EAS

AF:

0.208

Gnomad SAS

AF:

0.0460

Gnomad FIN

AF:

0.0313

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.00603

Gnomad OTH

AF:

0.0841

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

GnomAD4 genome

AF:

0.0907

AC:

13805

AN:

152194

Hom.:

1378

Cov.:

AF XY:

0.0955

AC XY:

7112

AN XY:

74436

show subpopulations

African (AFR)

AF:

0.201

AC:

8355

AN:

41484

American (AMR)

AF:

0.200

AC:

3064

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0444

AC:

154

AN:

3468

East Asian (EAS)

AF:

0.208

AC:

1077

AN:

5174

South Asian (SAS)

AF:

0.0460

AC:

222

AN:

4826

European-Finnish (FIN)

AF:

0.0313

AC:

332

AN:

10622

Middle Eastern (MID)

AF:

0.0510

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00601

AC:

409

AN:

68012

Other (OTH)

AF:

0.0837

AC:

177

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

570

1141

1711

2282

2852

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

134

268

402

536

670

<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:

0.0128

Hom.:

Bravo

AF:

0.110

Asia WGS

AF:

0.122

AC:

422

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

0.43

(source)

DANN

Benign

0.81

PhyloP100

-0.30

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over