rs11245007

chr10-126504416-C-T

Variant summary

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

The NM_001350921.2(C10orf90):c.1075G>A(p.Asp359Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 1,613,930 control chromosomes in the GnomAD database, including 93,769 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.40 (13894 hom., cov: 32)
  • Exomes 𝑓: 0.32 (79875 hom.)
• Consequence: C10orf90 NM_001350921.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.60

Genes affected

C10orf90 (HGNC:26563): (chromosome 10 open reading frame 90) Predicted to enable histone deacetylase binding activity; microtubule binding activity; and ubiquitin protein ligase activity. Predicted to be involved in several processes, including protein stabilization; regulation of cell cycle process; and response to ionizing radiation. Located in several cellular components, including cytoskeleton; cytosol; and nucleoplasm. [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 (MetaRNN=6.0354714E-6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C10orf90	NM_001350921.2	c.1075G>A	p.Asp359Asn	missense_variant	4/10	ENST00000488181.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C10orf90	ENST00000488181.3	c.1075G>A	p.Asp359Asn	missense_variant	4/10	2	NM_001350921.2	P2

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61014 AN: 151928 Hom.: 13856 Cov.: 32

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.377

GnomAD3 exomes AF: 0.372 AC: 93548 AN: 251316 Hom.: 19116 AF XY: 0.368 AC XY: 49937 AN XY: 135834

Gnomad AFR exome AF: 0.621

Gnomad AMR exome AF: 0.438

Gnomad ASJ exome AF: 0.366

Gnomad EAS exome AF: 0.510

Gnomad SAS exome AF: 0.464

Gnomad FIN exome AF: 0.269

Gnomad NFE exome AF: 0.292

Gnomad OTH exome AF: 0.340

GnomAD4 exome AF: 0.321 AC: 469720 AN: 1461884 Hom.: 79875 Cov.: 56 AF XY: 0.324 AC XY: 235296 AN XY: 727242

Gnomad4 AFR exome AF: 0.632

Gnomad4 AMR exome AF: 0.434

Gnomad4 ASJ exome AF: 0.364

Gnomad4 EAS exome AF: 0.487

Gnomad4 SAS exome AF: 0.451

Gnomad4 FIN exome AF: 0.270

Gnomad4 NFE exome AF: 0.291

Gnomad4 OTH exome AF: 0.347

GnomAD4 genome AF: 0.402 AC: 61113 AN: 152046 Hom.: 13894 Cov.: 32 AF XY: 0.403 AC XY: 29979 AN XY: 74320

Gnomad4 AFR AF: 0.612

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.465

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.381

Alfa AF: 0.329 Hom.: 15202

Bravo AF: 0.423

TwinsUK AF: 0.295 AC: 1095

ALSPAC AF: 0.298 AC: 1147

ESP6500AA AF: 0.595 AC: 2620

ESP6500EA AF: 0.302 AC: 2596

ExAC AF: 0.374 AC: 45369

Asia WGS AF: 0.494 AC: 1716 AN: 3478

EpiCase AF: 0.302

EpiControl AF: 0.296

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.055
BayesDel_addAF	Benign	-0.84	T
BayesDel_noAF	Benign	-0.84
Cadd	Benign	3.6
Dann	Benign	0.70
DEOGEN2	Benign	0.017	T;T;.
Eigen	Benign	-1.7
Eigen_PC	Benign	-1.5
FATHMM_MKL	Benign	0.0029	N
LIST_S2	Benign	0.20	T;T;T
MetaRNN	Benign	0.0000060	T;T;T
MetaSVM	Benign	-0.98	T
MutationAssessor	Benign	-2.1	N;.;.
MutationTaster	Benign	1.0	P;P;P;P;P;P
PROVEAN	Benign	1.1	N;N;N
REVEL	Benign	0.065
Sift	Benign	1.0	T;T;T
Sift4G	Benign	1.0	T;T;T
Polyphen		0.0	B;.;.
Vest4		0.053
MPC		0.074
ClinPred		0.00030	T
GERP RS		1.6
Varity_R		0.025
gMVP		0.056

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: rs11245007; hg19: chr10-128192985; COSMIC: COSV52949554; COSMIC: COSV52949554;