Genetic Variant ENST00000649703.2:n.211-9404A>G (chr6-39970688-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000649703.2(ENSG00000293066):n.211-9404A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0614 in 152,282 control chromosomes in the GnomAD database, including 541 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 0.061 ( 541 hom., cov: 32)

Consequence

ENSG00000293066
ENST00000649703.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.529

Publications

1 publications found

Variant links:

Genes affected

ENSG00000293066 (HGNC:):

ENSG00000293066 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=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723789	XR_001744112.1 link	n.260-4032A>G		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000293066	ENST00000649703.2 link	n.211-9404A>G	intron_variant	Intron 3 of 4
ENSG00000293066	ENST00000741538.1 link	n.257-9404A>G	intron_variant	Intron 3 of 5
ENSG00000293066	ENST00000741539.1 link	n.153+7129A>G	intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.0613

AC:

9328

AN:

152164

Hom.:

539

Cov.:

show subpopulations

Gnomad AFR

AF:

0.139

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0761

Gnomad ASJ

AF:

0.0265

Gnomad EAS

AF:

0.127

Gnomad SAS

AF:

0.0304

Gnomad FIN

AF:

0.00583

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.0190

Gnomad OTH

AF:

0.0708

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

GnomAD4 genome

AF:

0.0614

AC:

9344

AN:

152282

Hom.:

541

Cov.:

AF XY:

0.0610

AC XY:

4544

AN XY:

74458

show subpopulations

African (AFR)

AF:

0.139

AC:

5758

AN:

41526

American (AMR)

AF:

0.0762

AC:

1166

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0265

AC:

AN:

3472

East Asian (EAS)

AF:

0.127

AC:

658

AN:

5186

South Asian (SAS)

AF:

0.0305

AC:

147

AN:

4824

European-Finnish (FIN)

AF:

0.00583

AC:

AN:

10626

Middle Eastern (MID)

AF:

0.0578

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0190

AC:

1295

AN:

68034

Other (OTH)

AF:

0.0705

AC:

149

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

431

862

1292

1723

2154

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:

0.0464

Hom.:

Bravo

AF:

0.0701

Asia WGS

AF:

0.0730

AC:

253

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.52

(source)

DANN

Benign

0.31

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