dbSNP rs16967753: ENSG00000259846:n.535+1244C>T (chr16-64601500-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000808892.1(ENSG00000259846):n.535+1244C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0376 in 151,856 control chromosomes in the GnomAD database, including 278 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 0.038 ( 278 hom., cov: 32)

Consequence

ENSG00000259846
ENST00000808892.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.524

Publications

0 publications found

Variant links:

Genes affected

ENSG00000259846 (HGNC:):

ENSG00000259846 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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000259846	ENST00000808892.1 link	n.535+1244C>T	intron_variant	Intron 4 of 4
ENSG00000259846	ENST00000808893.1 link	n.521+1244C>T	intron_variant	Intron 4 of 4
ENSG00000259846	ENST00000808894.1 link	n.643+1244C>T	intron_variant	Intron 4 of 4
ENSG00000259846	ENST00000808895.1 link	n.609+1244C>T	intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes

AF:

0.0376

AC:

5700

AN:

151738

Hom.:

278

Cov.:

show subpopulations

Gnomad AFR

AF:

0.112

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0151

Gnomad ASJ

AF:

0.0144

Gnomad EAS

AF:

0.000195

Gnomad SAS

AF:

0.0933

Gnomad FIN

AF:

0.000471

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.00379

Gnomad OTH

AF:

0.0293

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

GnomAD4 genome

AF:

0.0376

AC:

5704

AN:

151856

Hom.:

278

Cov.:

AF XY:

0.0387

AC XY:

2875

AN XY:

74230

show subpopulations

African (AFR)

AF:

0.112

AC:

4644

AN:

41442

American (AMR)

AF:

0.0150

AC:

228

AN:

15202

Ashkenazi Jewish (ASJ)

AF:

0.0144

AC:

AN:

3464

East Asian (EAS)

AF:

0.000195

AC:

AN:

5128

South Asian (SAS)

AF:

0.0932

AC:

450

AN:

4830

European-Finnish (FIN)

AF:

0.000471

AC:

AN:

10612

Middle Eastern (MID)

AF:

0.0272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00379

AC:

257

AN:

67866

Other (OTH)

AF:

0.0290

AC:

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

262

524

787

1049

1311

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

180

240

300

<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:

0.0195

Hom.:

Bravo

AF:

0.0398

Asia WGS

AF:

0.0570

AC:

201

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.61

(source)

DANN

Benign

0.75

PhyloP100

-0.52

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