Genetic Variant ENSG00000285163:n.77+5897T>C (chr16-85930957-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 ENST00000646214.1(ENSG00000285163):n.77+5897T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,188 control chromosomes in the GnomAD database, including 1,772 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 0.15 ( 1772 hom., cov: 33)

Consequence

ENSG00000285163
ENST00000646214.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.229

Publications

6 publications found

Variant links:

Genes affected

ENSG00000285163 (HGNC:):

ENSG00000285163 links:

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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 (AMR) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285163	ENST00000646214.1 link	n.77+5897T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.148

AC:

22452

AN:

152070

Hom.:

1770

Cov.:

show subpopulations

Gnomad AFR

AF:

0.133

Gnomad AMI

AF:

0.0636

Gnomad AMR

AF:

0.183

Gnomad ASJ

AF:

0.0493

Gnomad EAS

AF:

0.137

Gnomad SAS

AF:

0.0650

Gnomad FIN

AF:

0.211

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.153

Gnomad OTH

AF:

0.132

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

GnomAD4 genome

AF:

0.148

AC:

22467

AN:

152188

Hom.:

1772

Cov.:

AF XY:

0.148

AC XY:

10979

AN XY:

74410

show subpopulations

African (AFR)

AF:

0.133

AC:

5513

AN:

41540

American (AMR)

AF:

0.184

AC:

2809

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0493

AC:

171

AN:

3470

East Asian (EAS)

AF:

0.138

AC:

712

AN:

5174

South Asian (SAS)

AF:

0.0649

AC:

313

AN:

4824

European-Finnish (FIN)

AF:

0.211

AC:

2230

AN:

10590

Middle Eastern (MID)

AF:

0.0272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.153

AC:

10377

AN:

67974

Other (OTH)

AF:

0.130

AC:

276

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

984

1968

2951

3935

4919

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

248

496

744

992

1240

<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:

0.151

Hom.:

3334

Bravo

AF:

0.149

Asia WGS

AF:

0.114

AC:

395

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

0.97

(source)

DANN

Benign

0.39

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