rs16867579

Variant names:

• chr8-101363039-A-C
• rs16867579
• ENST00000419462.1:n.285+961A>C

Variant summary

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

The ENST00000419462.1(NACA4P):​n.285+961A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,156 control chromosomes in the GnomAD database, including 2,528 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 0.11 (2528 hom., cov: 32)
• Consequence: NACA4P ENST00000419462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.838

Genes affected

NACA4P (HGNC:24688): (NACA family member 4, pseudogene) Predicted to enable unfolded protein binding activity. Predicted to be involved in protein targeting to membrane. Predicted to be part of nascent polypeptide-associated complex. Predicted to be active in cytoplasm. [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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NACA4P	ENST00000419462.1	n.285+961A>C		intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16192 AN: 152038 Hom.: 2504 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0537

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.00886

Gnomad SAS AF: 0.0197

Gnomad FIN AF: 0.00594

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.00898

Gnomad OTH AF: 0.0866

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

GnomAD4 genome AF: 0.107 AC: 16270 AN: 152156 Hom.: 2528 Cov.: 32 AF XY: 0.105 AC XY: 7783 AN XY: 74394

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.0535

Gnomad4 ASJ AF: 0.0516

Gnomad4 EAS AF: 0.00888

Gnomad4 SAS AF: 0.0188

Gnomad4 FIN AF: 0.00594

Gnomad4 NFE AF: 0.00898

Gnomad4 OTH AF: 0.0909

Alfa AF: 0.0318 Hom.: 480

Bravo AF: 0.122

Asia WGS AF: 0.0610 AC: 212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.70

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs16867579; hg19: chr8-102375267;