Genetic Variant ENSG00000300361:n.918-6611G>A (chr5-51868281-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 ENST00000771174.1(ENSG00000300361):n.918-6611G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0567 in 151,902 control chromosomes in the GnomAD database, including 272 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 0.057 ( 272 hom., cov: 32)

Consequence

ENSG00000300361
ENST00000771174.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.809

Publications

4 publications found

Variant links:

Genes affected

ENSG00000300361 (HGNC:):

ENSG00000300361 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=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0722 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
ENSG00000300361	ENST00000771174.1 link	n.918-6611G>A		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes

AF:

0.0567

AC:

8603

AN:

151784

Hom.:

272

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0429

Gnomad AMI

AF:

0.0208

Gnomad AMR

AF:

0.0528

Gnomad ASJ

AF:

0.0569

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.0303

Gnomad FIN

AF:

0.0452

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.0739

Gnomad OTH

AF:

0.0713

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

GnomAD4 genome

AF:

0.0567

AC:

8606

AN:

151902

Hom.:

272

Cov.:

AF XY:

0.0547

AC XY:

4063

AN XY:

74260

show subpopulations

African (AFR)

AF:

0.0428

AC:

1777

AN:

41480

American (AMR)

AF:

0.0527

AC:

803

AN:

15224

Ashkenazi Jewish (ASJ)

AF:

0.0569

AC:

197

AN:

3464

East Asian (EAS)

AF:

0.000579

AC:

AN:

5182

South Asian (SAS)

AF:

0.0307

AC:

148

AN:

4816

European-Finnish (FIN)

AF:

0.0452

AC:

479

AN:

10596

Middle Eastern (MID)

AF:

0.0646

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0739

AC:

5011

AN:

67822

Other (OTH)

AF:

0.0710

AC:

150

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

414

828

1243

1657

2071

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

200

300

400

500

<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:

0.0642

Hom.:

268

Bravo

AF:

0.0568

Asia WGS

AF:

0.0190

AC:

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

(source)

DANN

Benign

0.65

PhyloP100

0.81

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