Genetic Variant ENST00000646214.1:n.77+2896G>A (chr16-85927956-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 ENST00000646214.1(ENSG00000285163):n.77+2896G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,198 control chromosomes in the GnomAD database, including 1,437 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 0.12 ( 1437 hom., cov: 32)

Consequence

ENSG00000285163
ENST00000646214.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.83

Publications

3 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=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.197 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+2896G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.121

AC:

18333

AN:

152080

Hom.:

1435

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0356

Gnomad AMI

AF:

0.343

Gnomad AMR

AF:

0.126

Gnomad ASJ

AF:

0.202

Gnomad EAS

AF:

0.207

Gnomad SAS

AF:

0.140

Gnomad FIN

AF:

0.0934

Gnomad MID

AF:

0.165

Gnomad NFE

AF:

0.159

Gnomad OTH

AF:

0.149

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

GnomAD4 genome

AF:

0.120

AC:

18333

AN:

152198

Hom.:

1437

Cov.:

AF XY:

0.119

AC XY:

8844

AN XY:

74420

show subpopulations

African (AFR)

AF:

0.0356

AC:

1478

AN:

41526

American (AMR)

AF:

0.126

AC:

1927

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.202

AC:

700

AN:

3468

East Asian (EAS)

AF:

0.208

AC:

1074

AN:

5174

South Asian (SAS)

AF:

0.141

AC:

678

AN:

4814

European-Finnish (FIN)

AF:

0.0934

AC:

990

AN:

10602

Middle Eastern (MID)

AF:

0.170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.159

AC:

10810

AN:

68004

Other (OTH)

AF:

0.148

AC:

313

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

799

1599

2398

3198

3997

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

212

424

636

848

1060

<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:

0.134

Hom.:

2518

Bravo

AF:

0.121

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.34

(source)

DANN

Benign

0.58

PhyloP100

-1.8

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