2-27563321-A-T

Variant summary

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

The NM_032266.5(C2orf16):c.145-2016A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 141,702 control chromosomes in the GnomAD database, including 6,183 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 0.29 (6183 hom., cov: 27)
• Consequence: C2orf16 NM_032266.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320

Genes affected

C2orf16 (HGNC:25275): (SPATA31 subfamily H member 1) Located in extracellular exosome and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C2orf16	NM_032266.5	c.145-2016A>T		intron_variant		ENST00000447166.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C2orf16	ENST00000447166.3	c.145-2016A>T		intron_variant		3	NM_032266.5	P1

Frequencies

GnomAD3 genomes AF: 0.290 AC: 41069 AN: 141636 Hom.: 6180 Cov.: 27

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.335

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.290 AC: 41080 AN: 141702 Hom.: 6183 Cov.: 27 AF XY: 0.296 AC XY: 20391 AN XY: 68822

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.459

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.505

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.336

Alfa AF: 0.271 Hom.: 727

Bravo AF: 0.289

Asia WGS AF: 0.301 AC: 1049 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	7.4
Dann	Benign	0.55

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: rs10208529; hg19: chr2-27786188;