14-54620115-A-G

Variant names:

• chr14-54620115-A-G
• rs9285581
• NM_015589.6:c.196+52003A>G

Variant summary

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

The NM_015589.6(SAMD4A):​c.196+52003A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 151,726 control chromosomes in the GnomAD database, including 22,238 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 0.54 (22238 hom., cov: 30)
• Consequence: SAMD4A NM_015589.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360
• Publications: 4 publications found

Genes affected

SAMD4A (HGNC:23023): (sterile alpha motif domain containing 4A) Sterile alpha motifs (SAMs) in proteins such as SAMD4A are part of an RNA-binding domain that functions as a posttranscriptional regulator by binding to an RNA sequence motif known as the Smaug recognition element, which was named after the Drosophila Smaug protein (Baez and Boccaccio, 2005 [PubMed 16221671]).[supplied by OMIM, Mar 2008]

LOC112268133 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.849 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SAMD4A	NM_015589.6	c.196+52003A>G		intron_variant	Intron 2 of 12	ENST00000554335.6	NP_056404.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SAMD4A	ENST00000554335.6	c.196+52003A>G		intron_variant	Intron 2 of 12	5	NM_015589.6	ENSP00000452535.1

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81389 AN: 151610 Hom.: 22239 Cov.: 30

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.537 AC: 81426 AN: 151726 Hom.: 22238 Cov.: 30 AF XY: 0.544 AC XY: 40371 AN XY: 74146

African (AFR) AF: 0.492 AC: 20304 AN: 41278

American (AMR) AF: 0.549 AC: 8368 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1581 AN: 3468

East Asian (EAS) AF: 0.870 AC: 4495 AN: 5166

South Asian (SAS) AF: 0.560 AC: 2694 AN: 4814

European-Finnish (FIN) AF: 0.628 AC: 6609 AN: 10520

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.524 AC: 35614 AN: 67932

Other (OTH) AF: 0.538 AC: 1129 AN: 2100

Alfa AF: 0.528 Hom.: 39628

Bravo AF: 0.531

Asia WGS AF: 0.646 AC: 2245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.4
DANN	Benign	0.64
PhyloP100		-0.036
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: rs9285581; hg19: chr14-55086833;