dbSNP rs9940048: ENSG00000261261:n.94G>A (chr16-52629949-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 ENST00000564331.1(ENSG00000261261):n.94G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 151,678 control chromosomes in the GnomAD database, including 5,409 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 0.26 ( 5409 hom., cov: 32)

Exomes 𝑓: 0.50 ( 0 hom. )

Consequence

ENSG00000261261
ENST00000564331.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.566

Publications

4 publications found

Variant links:

Genes affected

ENSG00000261261 (HGNC:):

ENSG00000261261 links:

CASC16 (HGNC:48608): (cancer susceptibility 16)

CASC16 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=-0.71).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000261261	ENST00000564331.1 link	n.94G>A	non_coding_transcript_exon_variant	Exon 2 of 4	3
ENSG00000261261	ENST00000659170.1 link	n.488G>A	non_coding_transcript_exon_variant	Exon 2 of 4
ENSG00000261261	ENST00000666586.1 link	n.482G>A	non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.263

AC:

39925

AN:

151556

Hom.:

5406

Cov.:

show subpopulations

Gnomad AFR

AF:

0.303

Gnomad AMI

AF:

0.227

Gnomad AMR

AF:

0.235

Gnomad ASJ

AF:

0.357

Gnomad EAS

AF:

0.257

Gnomad SAS

AF:

0.223

Gnomad FIN

AF:

0.207

Gnomad MID

AF:

0.370

Gnomad NFE

AF:

0.253

Gnomad OTH

AF:

0.287

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.263

AC:

39944

AN:

151672

Hom.:

5409

Cov.:

AF XY:

0.259

AC XY:

19175

AN XY:

74098

show subpopulations

African (AFR)

AF:

0.302

AC:

12495

AN:

41316

American (AMR)

AF:

0.235

AC:

3577

AN:

15238

Ashkenazi Jewish (ASJ)

AF:

0.357

AC:

1238

AN:

3468

East Asian (EAS)

AF:

0.257

AC:

1321

AN:

5146

South Asian (SAS)

AF:

0.224

AC:

1072

AN:

4796

European-Finnish (FIN)

AF:

0.207

AC:

2171

AN:

10484

Middle Eastern (MID)

AF:

0.371

AC:

109

AN:

294

European-Non Finnish (NFE)

AF:

0.253

AC:

17156

AN:

67918

Other (OTH)

AF:

0.285

AC:

599

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1487

2974

4460

5947

7434

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

418

836

1254

1672

2090

<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:

0.252

Hom.:

638

Bravo

AF:

0.267

Asia WGS

AF:

0.226

AC:

787

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

(source)

DANN

Benign

0.76

PhyloP100

0.57

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