NM_001195124.3:c.*237C>G

Variant names:

• chr16-87302820-G-C
• NM_001195124.3:c.*237C>G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001195124.3(C16orf95):​c.*237C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000253 in 395,058 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000025 (0 hom.)
• Consequence: C16orf95 NM_001195124.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

Genes affected

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

ENSG00000131152 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000253 AC: 1 AN: 395058 Hom.: 0 Cov.: 3 AF XY: 0.00000478 AC XY: 1 AN XY: 209108

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.0000838

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.0
DANN	Benign	0.77

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr16-87336426;