Genetic Variant ENST00000666642.1:n.568+592A>G (chr1-34684573-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 ENST00000666642.1(ENSG00000287703):n.568+592A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 152,082 control chromosomes in the GnomAD database, including 4,289 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 0.23 ( 4289 hom., cov: 32)

Consequence

ENSG00000287703
ENST00000666642.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.225

Publications

8 publications found

Variant links:

Genes affected

ENSG00000287703 (HGNC:):

ENSG00000287703 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=-0.56).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105378641	XR_001737964.2 link	n.155+592A>G	intron_variant	Intron 1 of 8
LOC105378641	XR_001737965.2 link	n.155+592A>G	intron_variant	Intron 1 of 5
LOC105378641	XR_001737966.2 link	n.155+592A>G	intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287703	ENST00000666642.1 link	n.568+592A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.230

AC:

34931

AN:

151962

Hom.:

4275

Cov.:

show subpopulations

Gnomad AFR

AF:

0.280

Gnomad AMI

AF:

0.178

Gnomad AMR

AF:

0.321

Gnomad ASJ

AF:

0.148

Gnomad EAS

AF:

0.144

Gnomad SAS

AF:

0.185

Gnomad FIN

AF:

0.228

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.193

Gnomad OTH

AF:

0.240

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

GnomAD4 genome

AF:

0.230

AC:

34966

AN:

152082

Hom.:

4289

Cov.:

AF XY:

0.231

AC XY:

17204

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.280

AC:

11610

AN:

41454

American (AMR)

AF:

0.322

AC:

4919

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.148

AC:

513

AN:

3468

East Asian (EAS)

AF:

0.144

AC:

747

AN:

5176

South Asian (SAS)

AF:

0.185

AC:

892

AN:

4820

European-Finnish (FIN)

AF:

0.228

AC:

2409

AN:

10576

Middle Eastern (MID)

AF:

0.248

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.193

AC:

13143

AN:

67986

Other (OTH)

AF:

0.236

AC:

498

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1341

2682

4024

5365

6706

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

350

700

1050

1400

1750

<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:

0.221

Hom.:

1842

Bravo

AF:

0.243

Asia WGS

AF:

0.191

AC:

664

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

(source)

DANN

Benign

0.68

PhyloP100

0.23

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