Genetic Variant ENST00000667697.1:n.254+1164G>A (chr3-106203747-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000667697.1(ENSG00000287421):n.254+1164G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 145,300 control chromosomes in the GnomAD database, including 2,563 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 0.17 ( 2563 hom., cov: 29)

Consequence

ENSG00000287421
ENST00000667697.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0330

Publications

3 publications found

Variant links:

Genes affected

ENSG00000287421 (HGNC:):

ENSG00000287421 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=-0.91).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000287421	ENST00000667697.1 link	n.254+1164G>A	intron_variant	Intron 3 of 3
ENSG00000287421	ENST00000837046.1 link	n.265-1001G>A	intron_variant	Intron 3 of 3
ENSG00000308895	ENST00000837134.1 link	n.232+5336C>T	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.172

AC:

25011

AN:

145168

Hom.:

2560

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0478

Gnomad AMI

AF:

0.239

Gnomad AMR

AF:

0.184

Gnomad ASJ

AF:

0.194

Gnomad EAS

AF:

0.206

Gnomad SAS

AF:

0.346

Gnomad FIN

AF:

0.146

Gnomad MID

AF:

0.250

Gnomad NFE

AF:

0.230

Gnomad OTH

AF:

0.170

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

GnomAD4 genome

AF:

0.172

AC:

25021

AN:

145300

Hom.:

2563

Cov.:

AF XY:

0.174

AC XY:

12272

AN XY:

70676

show subpopulations

African (AFR)

AF:

0.0477

AC:

1859

AN:

38958

American (AMR)

AF:

0.184

AC:

2670

AN:

14524

Ashkenazi Jewish (ASJ)

AF:

0.194

AC:

660

AN:

3404

East Asian (EAS)

AF:

0.206

AC:

944

AN:

4574

South Asian (SAS)

AF:

0.347

AC:

1573

AN:

4534

European-Finnish (FIN)

AF:

0.146

AC:

1408

AN:

9614

Middle Eastern (MID)

AF:

0.239

AC:

AN:

272

European-Non Finnish (NFE)

AF:

0.230

AC:

15280

AN:

66524

Other (OTH)

AF:

0.174

AC:

351

AN:

2012

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.519

Heterozygous variant carriers

978

1957

2935

3914

4892

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

290

580

870

1160

1450

<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:

0.185

Hom.:

509

Bravo

AF:

0.159

Asia WGS

AF:

0.276

AC:

958

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.6

(source)

DANN

Benign

0.75

PhyloP100

0.033

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