Genetic Variant ENSG00000304165:n.218+12652C>T (chr6-65888301-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000800215.1(ENSG00000304165):n.218+12652C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 152,000 control chromosomes in the GnomAD database, including 9,956 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 0.34 ( 9956 hom., cov: 32)

Consequence

ENSG00000304165
ENST00000800215.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.190

Publications

7 publications found

Variant links:

Genes affected

ENSG00000304165 (HGNC:):

ENSG00000304165 links:

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new If you want to explore the variant's impact on the transcript ENST00000800215.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.93).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000800215.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304165	ENST00000800215.1		n.218+12652C>T		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.338

AC:

51285

AN:

151880

Hom.:

9957

Cov.:

show subpopulations

Gnomad AFR

AF:

0.155

Gnomad AMI

AF:

0.491

Gnomad AMR

AF:

0.305

Gnomad ASJ

AF:

0.484

Gnomad EAS

AF:

0.152

Gnomad SAS

AF:

0.295

Gnomad FIN

AF:

0.409

Gnomad MID

AF:

0.446

Gnomad NFE

AF:

0.451

Gnomad OTH

AF:

0.372

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

GnomAD4 genome

AF:

0.337

AC:

51290

AN:

152000

Hom.:

9956

Cov.:

AF XY:

0.332

AC XY:

24626

AN XY:

74272

show subpopulations

African (AFR)

AF:

0.155

AC:

6414

AN:

41496

American (AMR)

AF:

0.304

AC:

4631

AN:

15226

Ashkenazi Jewish (ASJ)

AF:

0.484

AC:

1681

AN:

3472

East Asian (EAS)

AF:

0.152

AC:

785

AN:

5158

South Asian (SAS)

AF:

0.296

AC:

1429

AN:

4822

European-Finnish (FIN)

AF:

0.409

AC:

4313

AN:

10556

Middle Eastern (MID)

AF:

0.456

AC:

134

AN:

294

European-Non Finnish (NFE)

AF:

0.451

AC:

30678

AN:

67956

Other (OTH)

AF:

0.369

AC:

780

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1628

3257

4885

6514

8142

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

514

1028

1542

2056

2570

<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:

0.432

Hom.:

23344

Bravo

AF:

0.322

Asia WGS

AF:

0.224

AC:

782

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

1.6

(source)

DANN

Benign

0.70

PhyloP100

0.19

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over