chr14-54656200-A-G

Variant names:

• chr14-54656200-A-G
• rs17127713
• NM_015589.6:c.197-45862A>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.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
• Publications: 5 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015589.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAMD4A	NM_015589.6	MANE Select	c.197-45862A>G		intron	N/A	NP_056404.4
	SAMD4A	NM_001161576.2		c.197-45862A>G		intron	N/A	NP_001155048.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAMD4A	ENST00000554335.6	TSL:5 MANE Select	c.197-45862A>G		intron	N/A	ENSP00000452535.1
	SAMD4A	ENST00000251091.9	TSL:1	c.197-45862A>G		intron	N/A	ENSP00000251091.5
	SAMD4A	ENST00000555112.1	TSL:1	n.482-45862A>G		intron	N/A

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

African (AFR) AF: 0.110 AC: 4558 AN: 41482

American (AMR) AF: 0.0361 AC: 552 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0557 AC: 193 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5180

South Asian (SAS) AF: 0.00705 AC: 34 AN: 4822

European-Finnish (FIN) AF: 0.00330 AC: 35 AN: 10594

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0236 AC: 1605 AN: 67988

Other (OTH) AF: 0.0559 AC: 118 AN: 2110

Alfa AF: 0.0470 Hom.: 210

Bravo AF: 0.0531

Asia WGS AF: 0.0140 AC: 49 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.38
DANN	Benign	0.66
PhyloP100		-0.33
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs17127713; hg19: chr14-55122918;