5-34698588-C-T

Variant names:

• chr5-34698588-C-T
• rs889319
• NM_015577.3:c.36+11633C>T

Variant summary

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

The NM_015577.3(RAI14):​c.36+11633C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 151,692 control chromosomes in the GnomAD database, including 21,270 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 0.52 (21270 hom., cov: 30)
• Consequence: RAI14 NM_015577.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106
• Publications: 2 publications found

Genes affected

RAI14 (HGNC:14873): (retinoic acid induced 14) Predicted to enable actin binding activity. Predicted to be involved in several processes, including apoptotic signaling pathway; regulation of NIK/NF-kappaB signaling; and spermatogenesis. Located in cytosol; fibrillar center; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAI14	NM_015577.3	c.36+11633C>T		intron_variant	Intron 2 of 17	ENST00000265109.8	NP_056392.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAI14	ENST00000265109.8	c.36+11633C>T		intron_variant	Intron 2 of 17	1	NM_015577.3	ENSP00000265109.3

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79238 AN: 151574 Hom.: 21225 Cov.: 30

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.587

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.523 AC: 79336 AN: 151692 Hom.: 21270 Cov.: 30 AF XY: 0.519 AC XY: 38454 AN XY: 74120

African (AFR) AF: 0.654 AC: 27043 AN: 41354

American (AMR) AF: 0.462 AC: 7049 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.570 AC: 1976 AN: 3466

East Asian (EAS) AF: 0.381 AC: 1943 AN: 5104

South Asian (SAS) AF: 0.395 AC: 1892 AN: 4792

European-Finnish (FIN) AF: 0.451 AC: 4749 AN: 10520

Middle Eastern (MID) AF: 0.597 AC: 173 AN: 290

European-Non Finnish (NFE) AF: 0.484 AC: 32890 AN: 67902

Other (OTH) AF: 0.542 AC: 1145 AN: 2112

Alfa AF: 0.493 Hom.: 34821

Bravo AF: 0.529

Asia WGS AF: 0.437 AC: 1520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.42
PhyloP100		-0.11
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: rs889319; hg19: chr5-34698693;