rs334908

Positions:

• chr5-34752352-A-G
• chr5-34752352-A-T

Variant summary

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

The NM_015577.3(RAI14):​c.37-5116A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 152,006 control chromosomes in the GnomAD database, including 25,815 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 0.58 (25815 hom., cov: 32)
• Consequence: RAI14 NM_015577.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.466

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RAI14	NM_015577.3	c.37-5116A>G		intron_variant		ENST00000265109.8	NP_056392.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RAI14	ENST00000265109.8	c.37-5116A>G		intron_variant		1	NM_015577.3	ENSP00000265109	P3

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87543 AN: 151892 Hom.: 25794 Cov.: 32

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.576 AC: 87608 AN: 152006 Hom.: 25815 Cov.: 32 AF XY: 0.573 AC XY: 42538 AN XY: 74286

Gnomad4 AFR AF: 0.703

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.589

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.517

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.536

Gnomad4 OTH AF: 0.574

Alfa AF: 0.547 Hom.: 4623

Bravo AF: 0.584

Asia WGS AF: 0.506 AC: 1762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.9
DANN	Benign	0.69

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: rs334908; hg19: chr5-34752457;