14-54729868-T-G

Variant names:

• chr14-54729868-T-G
• rs4898848
• NM_015589.6:c.716-7156T>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.716-7156T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 151,954 control chromosomes in the GnomAD database, including 9,876 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 0.35 (9876 hom., cov: 32)
• Consequence: SAMD4A NM_015589.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23
• Publications: 1 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.418 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAMD4A	NM_015589.6	MANE Select	c.716-7156T>G		intron	N/A	NP_056404.4	Q9UPU9-1
	SAMD4A	NM_001161576.2		c.716-18947T>G		intron	N/A	NP_001155048.2	Q9UPU9-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAMD4A	ENST00000554335.6	TSL:5 MANE Select	c.716-7156T>G		intron	N/A	ENSP00000452535.1	Q9UPU9-1
	SAMD4A	ENST00000251091.9	TSL:1	c.716-18947T>G		intron	N/A	ENSP00000251091.5	Q9UPU9-3
	SAMD4A	ENST00000557013.1	TSL:1	n.3440-5072T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53841 AN: 151836 Hom.: 9866 Cov.: 32

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.355 AC: 53883 AN: 151954 Hom.: 9876 Cov.: 32 AF XY: 0.355 AC XY: 26328 AN XY: 74264

African (AFR) AF: 0.423 AC: 17522 AN: 41424

American (AMR) AF: 0.271 AC: 4142 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1114 AN: 3468

East Asian (EAS) AF: 0.290 AC: 1497 AN: 5166

South Asian (SAS) AF: 0.306 AC: 1473 AN: 4820

European-Finnish (FIN) AF: 0.385 AC: 4057 AN: 10526

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.340 AC: 23091 AN: 67962

Other (OTH) AF: 0.330 AC: 698 AN: 2112

Alfa AF: 0.339 Hom.: 4904

Bravo AF: 0.349

Asia WGS AF: 0.306 AC: 1060 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	13
DANN	Benign	0.61
PhyloP100		1.2
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: rs4898848; hg19: chr14-55196586;