Genetic Variant ENSG00000305332:n.94-3816T>C (chr6-24116622-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 ENST00000810475.1(ENSG00000305332):n.94-3816T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0414 in 98,652 control chromosomes in the GnomAD database, including 90 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 0.041 ( 90 hom., cov: 33)

Consequence

ENSG00000305332
ENST00000810475.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.534

Publications

2 publications found

Variant links:

Genes affected

ENSG00000305332 (HGNC:):

ENSG00000305332 links:

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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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0884 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
ENSG00000305332	ENST00000810475.1 link	n.94-3816T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0415

AC:

4087

AN:

98554

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0918

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0282

Gnomad ASJ

AF:

0.00466

Gnomad EAS

AF:

0.000306

Gnomad SAS

AF:

0.000466

Gnomad FIN

AF:

0.00649

Gnomad MID

AF:

0.0225

Gnomad NFE

AF:

0.0265

Gnomad OTH

AF:

0.0398

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

GnomAD4 genome

AF:

0.0414

AC:

4084

AN:

98652

Hom.:

Cov.:

AF XY:

0.0393

AC XY:

1849

AN XY:

47016

show subpopulations

African (AFR)

AF:

0.0914

AC:

2481

AN:

27154

American (AMR)

AF:

0.0281

AC:

251

AN:

8928

Ashkenazi Jewish (ASJ)

AF:

0.00466

AC:

AN:

2574

East Asian (EAS)

AF:

0.000307

AC:

AN:

3254

South Asian (SAS)

AF:

0.000466

AC:

AN:

2146

European-Finnish (FIN)

AF:

0.00649

AC:

AN:

5238

Middle Eastern (MID)

AF:

0.0245

AC:

AN:

204

European-Non Finnish (NFE)

AF:

0.0265

AC:

1247

AN:

47120

Other (OTH)

AF:

0.0394

AC:

AN:

1320

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

211

421

632

842

1053

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

160

200

<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:

0.0225

Hom.:

Bravo

AF:

0.0291

Asia WGS

AF:

0.00173

AC:

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

3.9

(source)

DANN

Benign

0.38

PhyloP100

0.53

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