Genetic Variant ENST00000782001.1:n.361-75A>T (chr7-83738461-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000782001.1(ENSG00000301806):n.361-75A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0666 in 152,032 control chromosomes in the GnomAD database, including 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 0.067 ( 763 hom., cov: 32)

Consequence

ENSG00000301806
ENST00000782001.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.02

Publications

0 publications found

Variant links:

Genes affected

ENSG00000301806 (HGNC:):

ENSG00000301806 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=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000301806	ENST00000782001.1 link	n.361-75A>T	intron_variant	Intron 6 of 6
ENSG00000301806	ENST00000782002.1 link	n.409-75A>T	intron_variant	Intron 7 of 7
ENSG00000301806	ENST00000782003.1 link	n.299-75A>T	intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes

AF:

0.0665

AC:

10105

AN:

151928

Hom.:

760

Cov.:

show subpopulations

Gnomad AFR

AF:

0.185

Gnomad AMI

AF:

0.00549

Gnomad AMR

AF:

0.0419

Gnomad ASJ

AF:

0.0130

Gnomad EAS

AF:

0.000386

Gnomad SAS

AF:

0.0255

Gnomad FIN

AF:

0.00598

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0216

Gnomad OTH

AF:

0.0584

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

GnomAD4 genome

AF:

0.0666

AC:

10126

AN:

152032

Hom.:

763

Cov.:

AF XY:

0.0646

AC XY:

4799

AN XY:

74318

show subpopulations

African (AFR)

AF:

0.185

AC:

7650

AN:

41444

American (AMR)

AF:

0.0417

AC:

638

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0130

AC:

AN:

3466

East Asian (EAS)

AF:

0.000386

AC:

AN:

5176

South Asian (SAS)

AF:

0.0253

AC:

122

AN:

4816

European-Finnish (FIN)

AF:

0.00598

AC:

AN:

10536

Middle Eastern (MID)

AF:

0.0408

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0216

AC:

1468

AN:

67998

Other (OTH)

AF:

0.0575

AC:

121

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

421

841

1262

1682

2103

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

102

204

306

408

510

<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:

0.0489

Hom.:

Bravo

AF:

0.0747

Asia WGS

AF:

0.0170

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

7.1

(source)

DANN

Benign

0.60

PhyloP100

1.0

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