16-87302820-G-C

Variant names:

• chr16-87302820-G-C
• rs1862788
• NM_001195124.3:c.*237C>G

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 0 publications found

Genes affected

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

ENSG00000131152 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001195124.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C16orf95	NM_001195124.3	MANE Select	c.*237C>G		3_prime_UTR	Exon 7 of 7	NP_001182053.1	H3BNZ7
	C16orf95	NM_001195125.3		c.*296C>G		3_prime_UTR	Exon 5 of 5	NP_001182054.1	Q9H693
	C16orf95	NM_001256917.2		c.*296C>G		3_prime_UTR	Exon 5 of 5	NP_001243846.1	A0A087X224

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C16orf95	ENST00000567970.2	TSL:5 MANE Select	c.*237C>G		3_prime_UTR	Exon 7 of 7	ENSP00000455079.2	H3BNZ7
	C16orf95	ENST00000253461.8	TSL:1	c.*296C>G		3_prime_UTR	Exon 5 of 5	ENSP00000253461.4	Q9H693
	C16orf95	ENST00000931586.1		c.*237C>G		3_prime_UTR	Exon 6 of 6	ENSP00000601645.1

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

African (AFR) AF: 0.00 AC: 0 AN: 11014

American (AMR) AF: 0.00 AC: 0 AN: 18426

Ashkenazi Jewish (ASJ) AF: 0.0000838 AC: 1 AN: 11940

East Asian (EAS) AF: 0.00 AC: 0 AN: 26360

South Asian (SAS) AF: 0.00 AC: 0 AN: 43904

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 24696

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1668

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 234632

Other (OTH) AF: 0.00 AC: 0 AN: 22418

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.0
DANN	Benign	0.77
PhyloP100		0.35

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

Other links and lift over

dbSNP: rs1862788; hg19: chr16-87336426;