dbSNP rs56073218: C15orf48:c.*41C>G (chr15-45433057-C-G) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_197955.3(C15orf48):c.*41C>G variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.00131 in 1,548,228 control chromosomes in the GnomAD database, including 2 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 0.00093 ( 1 hom., cov: 33)

Exomes 𝑓: 0.0013 ( 1 hom. )

Consequence

C15orf48
NM_197955.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.75

Variant links:

Genes affected

C15orf48 (HGNC:29898): (chromosome 15 open reading frame 48) This gene was first identified in a study of human esophageal squamous cell carcinoma tissues. Levels of both the message and protein are reduced in carcinoma samples. In adult human tissues, this gene is expressed in the the esophagus, stomach, small intestine, colon and placenta. Alternatively spliced transcript variants that encode the same protein have been identified. [provided by RefSeq, Jun 2012]

C15orf48 links:

MIR147B (HGNC:33655): (microRNA 147b) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

MIR147B links:

ENSG00000259342 (HGNC:):

ENSG00000259342 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.27).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C15orf48	NM_197955.3 link	c.*41C>G		3_prime_UTR_variant	Exon 5 of 5	ENST00000396650.7	NP_922946.1	Q9C002A0A024R5U4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C15orf48	ENST00000396650.7 link	c.*41C>G		3_prime_UTR_variant	Exon 5 of 5	1	NM_197955.3	ENSP00000379887.2		Q9C002

Frequencies

GnomAD3 genomes

AF:

0.000929

AC:

141

AN:

151856

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000315

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000657

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00228

Gnomad FIN

AF:

0.000570

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00160

Gnomad OTH

AF:

0.000479

GnomAD3 exomes

AF:

0.000859

AC:

216

AN:

251346

Hom.:

AF XY:

0.000868

AC XY:

118

AN XY:

135870

show subpopulations

Gnomad AFR exome

AF:

0.000369

Gnomad AMR exome

AF:

0.000260

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00118

Gnomad FIN exome

AF:

0.00102

Gnomad NFE exome

AF:

0.00123

Gnomad OTH exome

AF:

0.000489

GnomAD4 exome

AF:

0.00135

AC:

1881

AN:

1396254

Hom.:

Cov.:

AF XY:

0.00135

AC XY:

940

AN XY:

698452

show subpopulations

Gnomad4 AFR exome

AF:

0.000251

Gnomad4 AMR exome

AF:

0.000247

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000254

Gnomad4 SAS exome

AF:

0.00130

Gnomad4 FIN exome

AF:

0.000637

Gnomad4 NFE exome

AF:

0.00157

Gnomad4 OTH exome

AF:

0.00110

GnomAD4 genome

AF:

0.000928

AC:

141

AN:

151974

Hom.:

Cov.:

AF XY:

0.000862

AC XY:

AN XY:

74286

show subpopulations

Gnomad4 AFR

AF:

0.000314

Gnomad4 AMR

AF:

0.0000656

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00228

Gnomad4 FIN

AF:

0.000570

Gnomad4 NFE

AF:

0.00160

Gnomad4 OTH

AF:

0.000474

Alfa

AF:

0.000974

Hom.:

Bravo

AF:

0.000869

Asia WGS

AF:

0.000289

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.27

CADD

Benign

DANN

Benign

0.87

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over