rs3816325

Variant names:

• chr5-34682662-A-G
• rs3816325
• NM_015577.3:c.-48-4210A>G

Variant summary

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

The NM_015577.3(RAI14):​c.-48-4210A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,208 control chromosomes in the GnomAD database, including 2,264 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 0.16 (2264 hom., cov: 32)
• Consequence: RAI14 NM_015577.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.411
• 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]

RAI14-DT (HGNC:55983): (RAI14 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAI14	NM_015577.3	c.-48-4210A>G		intron_variant	Intron 1 of 17	ENST00000265109.8	NP_056392.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAI14	ENST00000265109.8	c.-48-4210A>G		intron_variant	Intron 1 of 17	1	NM_015577.3	ENSP00000265109.3

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24763 AN: 152090 Hom.: 2265 Cov.: 32

Gnomad AFR AF: 0.0901

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.0932

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.163 AC: 24757 AN: 152208 Hom.: 2264 Cov.: 32 AF XY: 0.159 AC XY: 11830 AN XY: 74396

African (AFR) AF: 0.0901 AC: 3741 AN: 41542

American (AMR) AF: 0.183 AC: 2794 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 812 AN: 3472

East Asian (EAS) AF: 0.303 AC: 1564 AN: 5154

South Asian (SAS) AF: 0.0929 AC: 448 AN: 4824

European-Finnish (FIN) AF: 0.126 AC: 1338 AN: 10594

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13463 AN: 68012

Other (OTH) AF: 0.187 AC: 395 AN: 2112

Alfa AF: 0.189 Hom.: 4823

Bravo AF: 0.169

Asia WGS AF: 0.137 AC: 478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.68
DANN	Benign	0.41
PhyloP100		-0.41
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: rs3816325; hg19: chr5-34682767;