chr4-139318541-A-G

Variant names:

• chr4-139318541-A-G
• rs7673213
• NM_057175.5:c.55-15633A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_057175.5(NAA15):​c.55-15633A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,078 control chromosomes in the GnomAD database, including 4,132 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 0.22 (4132 hom., cov: 32)
  • Exomes 𝑓: 0.33 (0 hom.)
• Consequence: NAA15 NM_057175.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238
• Publications: 4 publications found

Genes affected

NAA15 (HGNC:30782): (N-alpha-acetyltransferase 15, NatA auxiliary subunit) N-alpha-acetylation is among the most common post-translational protein modifications in eukaryotic cells. This process involves the transfer of an acetyl group from acetyl-coenzyme A to the alpha-amino group on a nascent polypeptide and is essential for normal cell function. This gene encodes the auxillary subunit of the N-terminal acetyltransferase A (NatA) complex. [provided by RefSeq, Jan 2017]

RNU6-1214P (HGNC:48177): (RNA, U6 small nuclear 1214, pseudogene)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_057175.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAA15	NM_057175.5	MANE Select	c.55-15633A>G		intron	N/A	NP_476516.1
	NAA15	NM_001410842.1		c.55-15633A>G		intron	N/A	NP_001397771.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAA15	ENST00000296543.10	TSL:1 MANE Select	c.55-15633A>G		intron	N/A	ENSP00000296543.4
	NAA15	ENST00000398947.1	TSL:5	c.55-15633A>G		intron	N/A	ENSP00000381920.1
	NAA15	ENST00000700277.1		c.55-15633A>G		intron	N/A	ENSP00000514913.1

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33789 AN: 151954 Hom.: 4128 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.220

GnomAD4 exome AF: 0.333 AC: 2 AN: 6 Hom.: 0 AF XY: 0.333 AC XY: 2 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 1 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.222 AC: 33803 AN: 152072 Hom.: 4132 Cov.: 32 AF XY: 0.222 AC XY: 16516 AN XY: 74352

African (AFR) AF: 0.310 AC: 12834 AN: 41456

American (AMR) AF: 0.152 AC: 2323 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 868 AN: 3470

East Asian (EAS) AF: 0.261 AC: 1349 AN: 5176

South Asian (SAS) AF: 0.393 AC: 1898 AN: 4826

European-Finnish (FIN) AF: 0.199 AC: 2102 AN: 10580

Middle Eastern (MID) AF: 0.288 AC: 84 AN: 292

European-Non Finnish (NFE) AF: 0.172 AC: 11675 AN: 67982

Other (OTH) AF: 0.221 AC: 467 AN: 2112

Alfa AF: 0.198 Hom.: 678

Bravo AF: 0.219

Asia WGS AF: 0.301 AC: 1048 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.6
DANN	Benign	0.65
PhyloP100		0.24
Mutation Taster		=100/0	polymorphism (auto)

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: rs7673213; hg19: chr4-140239695;