rs17127713

chr14-54656200-A-G

Variant summary

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

The NM_015589.6(SAMD4A):c.197-45862A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0472 in 152,140 control chromosomes in the GnomAD database, including 277 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 0.047 (277 hom., cov: 32)
• Consequence: SAMD4A NM_015589.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.325

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SAMD4A	NM_015589.6	c.197-45862A>G		intron_variant		ENST00000554335.6
LOC112268133	XR_002957606.2	n.47095A>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SAMD4A	ENST00000554335.6	c.197-45862A>G		intron_variant		5	NM_015589.6	A1

Frequencies

GnomAD3 genomes AF: 0.0471 AC: 7163 AN: 152022 Hom.: 276 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.0361

Gnomad ASJ AF: 0.0557

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00725

Gnomad FIN AF: 0.00330

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0236

Gnomad OTH AF: 0.0565

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

GnomAD4 genome AF: 0.0472 AC: 7179 AN: 152140 Hom.: 277 Cov.: 32 AF XY: 0.0452 AC XY: 3361 AN XY: 74384

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.0361

Gnomad4 ASJ AF: 0.0557

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00705

Gnomad4 FIN AF: 0.00330

Gnomad4 NFE AF: 0.0236

Gnomad4 OTH AF: 0.0559

Alfa AF: 0.0346 Hom.: 46

Bravo AF: 0.0531

Asia WGS AF: 0.0140 AC: 49 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	0.38
Dann	Benign	0.66
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs17127713; hg19: chr14-55122918;