rs1862788

Positions:

• chr16-87302820-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

Genes affected

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

C16orf95 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C16orf95	NM_001195124.3	c.*237C>T		3_prime_UTR_variant	7/7	ENST00000567970.2	NP_001182053.1
C16orf95	NM_001195125.3	c.*296C>T		3_prime_UTR_variant	5/5		NP_001182054.1
C16orf95	NM_001256917.2	c.*296C>T		3_prime_UTR_variant	5/5		NP_001243846.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C16orf95	ENST00000567970.2	c.*237C>T		3_prime_UTR_variant	7/7	5	NM_001195124.3	ENSP00000455079.2

Frequencies

GnomAD3 genomes AF: 0.0755 AC: 11475 AN: 152082 Hom.: 1305 Cov.: 32

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.: 3 AF XY: 0.0129 AC XY: 2695 AN XY: 209084

Gnomad4 AFR exome AF: 0.242

Gnomad4 AMR exome AF: 0.0219

Gnomad4 ASJ exome AF: 0.0350

Gnomad4 EAS exome AF: 0.0000379

Gnomad4 SAS exome AF: 0.00683

Gnomad4 FIN exome AF: 0.00166

Gnomad4 NFE exome AF: 0.00482

Gnomad4 OTH exome AF: 0.0258

GnomAD4 genome AF: 0.0758 AC: 11531 AN: 152200 Hom.: 1316 Cov.: 32 AF XY: 0.0725 AC XY: 5396 AN XY: 74438

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.0339

Gnomad4 ASJ AF: 0.0349

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00580

Gnomad4 FIN AF: 0.00113

Gnomad4 NFE AF: 0.00495

Gnomad4 OTH AF: 0.0640

Alfa AF: 0.0187 Hom.: 257

Bravo AF: 0.0851

Asia WGS AF: 0.0180 AC: 64 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
DANN	Benign	0.80

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

Other links and lift over

dbSNP: rs1862788; hg19: chr16-87336426;