Genetic Variant C16orf95:c.*237C>T (chr16-87302820-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 NM_001195124.3(C16orf95):c.*237C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0313 in 547,198 control chromosomes in the GnomAD database, including 1,680 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 0.076 ( 1316 hom., cov: 32)

Exomes 𝑓: 0.014 ( 364 hom. )

Consequence

C16orf95
NM_001195124.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.347

Publications

2 publications found

Variant links:

Genes affected

C16orf95 (HGNC:40033): (chromosome 16 open reading frame 95)

C16orf95 links:

ENSG00000131152 (HGNC:):

ENSG00000131152 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=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
C16orf95	NM_001195124.3 link	c.*237C>T	3_prime_UTR_variant	Exon 7 of 7	ENST00000567970.2	NP_001182053.1	H3BNZ7
C16orf95	NM_001195125.3 link	c.*296C>T	3_prime_UTR_variant	Exon 5 of 5		NP_001182054.1	Q9H693
C16orf95	NM_001256917.2 link	c.*296C>T	3_prime_UTR_variant	Exon 5 of 5		NP_001243846.1	A0A087X224

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C16orf95	ENST00000567970.2 link	c.*237C>T		3_prime_UTR_variant	Exon 7 of 7	5	NM_001195124.3	ENSP00000455079.2		H3BNZ7
ENSG00000131152	ENST00000568879.1 link	c.*296C>T		downstream_gene_variant		4		ENSP00000454386.1		H3BMH7

Frequencies

GnomAD3 genomes

AF:

0.0755

AC:

11475

AN:

152082

Hom.:

1305

Cov.:

show subpopulations

Gnomad AFR

AF:

0.249

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0341

Gnomad ASJ

AF:

0.0349

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00538

Gnomad FIN

AF:

0.00113

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.00495

Gnomad OTH

AF:

0.0647

GnomAD4 exome

AF:

0.0142

AC:

5594

AN:

394998

Hom.:

364

Cov.:

AF XY:

0.0129

AC XY:

2695

AN XY:

209084

show subpopulations

African (AFR)

AF:

0.242

AC:

2658

AN:

10982

American (AMR)

AF:

0.0219

AC:

404

AN:

18416

Ashkenazi Jewish (ASJ)

AF:

0.0350

AC:

418

AN:

11938

East Asian (EAS)

AF:

0.0000379

AC:

AN:

26360

South Asian (SAS)

AF:

0.00683

AC:

300

AN:

43904

European-Finnish (FIN)

AF:

0.00166

AC:

AN:

24696

Middle Eastern (MID)

AF:

0.0372

AC:

AN:

1668

European-Non Finnish (NFE)

AF:

0.00482

AC:

1131

AN:

234622

Other (OTH)

AF:

0.0258

AC:

579

AN:

22412

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

241

482

722

963

1204

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

104

156

208

260

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0758

AC:

11531

AN:

152200

Hom.:

1316

Cov.:

AF XY:

0.0725

AC XY:

5396

AN XY:

74438

show subpopulations

African (AFR)

AF:

0.250

AC:

10359

AN:

41478

American (AMR)

AF:

0.0339

AC:

519

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0349

AC:

121

AN:

3468

East Asian (EAS)

AF:

0.00

AC:

AN:

5182

South Asian (SAS)

AF:

0.00580

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.00113

AC:

AN:

10616

Middle Eastern (MID)

AF:

0.0646

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00495

AC:

337

AN:

68024

Other (OTH)

AF:

0.0640

AC:

135

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

441

881

1322

1762

2203

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

106

212

318

424

530

<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:

0.0265

Hom.:

532

Bravo

AF:

0.0851

Asia WGS

AF:

0.0180

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

9.6

(source)

DANN

Benign

0.80

PhyloP100

0.35

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over