rs10512170

Positions:

• chr9-85987480-G-A
• chr9-85987480-G-C
• chr9-85987480-G-T

Variant summary

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

The NM_024635.4(NAA35):​c.878-8919G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 152,146 control chromosomes in the GnomAD database, including 3,793 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 0.14 (3793 hom., cov: 32)
• Consequence: NAA35 NM_024635.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204

Genes affected

NAA35 (HGNC:24340): (N-alpha-acetyltransferase 35, NatC auxiliary subunit) Involved in negative regulation of apoptotic process. Located in cytosol; nucleoplasm; and plasma membrane. Part of NatC complex. Colocalizes with polysome. [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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NAA35	NM_024635.4	c.878-8919G>A		intron_variant		ENST00000361671.10	NP_078911.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NAA35	ENST00000361671.10	c.878-8919G>A		intron_variant		1	NM_024635.4	ENSP00000354972	P1

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20763 AN: 152028 Hom.: 3779 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0742

Gnomad ASJ AF: 0.0337

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.00537

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00582

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.137 AC: 20833 AN: 152146 Hom.: 3793 Cov.: 32 AF XY: 0.137 AC XY: 10226 AN XY: 74390

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.0743

Gnomad4 ASJ AF: 0.0337

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.00537

Gnomad4 NFE AF: 0.00582

Gnomad4 OTH AF: 0.104

Alfa AF: 0.0806 Hom.: 558

Bravo AF: 0.158

Asia WGS AF: 0.227 AC: 791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.1
DANN	Benign	0.92

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: rs10512170; hg19: chr9-88602395;