Genetic Variant ENSG00000302585:n.181-39946T>C (chr6-71647057-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 ENST00000787970.1(ENSG00000302585):n.181-39946T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,084 control chromosomes in the GnomAD database, including 1,763 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 ( 1763 hom., cov: 33)

Consequence

ENSG00000302585
ENST00000787970.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.308

Publications

7 publications found

Variant links:

Genes affected

ENSG00000302585 (HGNC:):

ENSG00000302585 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=-0.89).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.222 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
ENSG00000302585	ENST00000787970.1 link	n.181-39946T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.134

AC:

20386

AN:

151968

Hom.:

1750

Cov.:

show subpopulations

Gnomad AFR

AF:

0.207

Gnomad AMI

AF:

0.204

Gnomad AMR

AF:

0.228

Gnomad ASJ

AF:

0.0502

Gnomad EAS

AF:

0.165

Gnomad SAS

AF:

0.0745

Gnomad FIN

AF:

0.0698

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.0846

Gnomad OTH

AF:

0.125

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

GnomAD4 genome

AF:

0.134

AC:

20441

AN:

152084

Hom.:

1763

Cov.:

AF XY:

0.134

AC XY:

9995

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.207

AC:

8596

AN:

41482

American (AMR)

AF:

0.228

AC:

3486

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.0502

AC:

174

AN:

3468

East Asian (EAS)

AF:

0.164

AC:

849

AN:

5166

South Asian (SAS)

AF:

0.0740

AC:

356

AN:

4810

European-Finnish (FIN)

AF:

0.0698

AC:

738

AN:

10568

Middle Eastern (MID)

AF:

0.112

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0845

AC:

5749

AN:

68002

Other (OTH)

AF:

0.130

AC:

274

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

866

1732

2597

3463

4329

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:

0.0914

Hom.:

397

Bravo

AF:

0.153

Asia WGS

AF:

0.173

AC:

603

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

3.5

(source)

DANN

Benign

0.68

PhyloP100

0.31

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