Genetic Variant ENSG00000301349:n.248+7402T>A (chr12-97245366-A-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000778372.1(ENSG00000301349):n.248+7402T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000109 in 366,000 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)

Exomes 𝑓: 0.000011 ( 0 hom. )

Consequence

ENSG00000301349
ENST00000778372.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.801

Publications

9 publications found

Variant links:

Genes affected

ENSG00000301349 (HGNC:):

ENSG00000301349 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC101928912	XR_246024.4 link	n.223+7402T>A	intron_variant	Intron 2 of 2
LOC101928912	XR_945251.3 link	n.224-1644T>A	intron_variant	Intron 2 of 3
LOC101928912	XR_945252.3 link	n.224-4304T>A	intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301349	ENST00000778372.1 link	n.248+7402T>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.00000439

AC:

AN:

227740

AF XY:

0.00000794

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000109

AC:

AN:

366000

Hom.:

Cov.:

AF XY:

0.0000191

AC XY:

AN XY:

209926

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

10392

American (AMR)

AF:

0.00

AC:

AN:

36234

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

11704

East Asian (EAS)

AF:

0.00

AC:

AN:

13130

South Asian (SAS)

AF:

0.0000600

AC:

AN:

66710

European-Finnish (FIN)

AF:

0.00

AC:

AN:

16852

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2846

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

191556

Other (OTH)

AF:

0.00

AC:

AN:

16576

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.538

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

(source)

DANN

Benign

0.63

PhyloP100

0.80

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over