14-54729868-T-G

Position:

• chr14-54729868-T-G

Variant summary

Our verdict is Benign. Variant got -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

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]

SAMD4A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SAMD4A	NM_015589.6	c.716-7156T>G		intron_variant		ENST00000554335.6	NP_056404.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SAMD4A	ENST00000554335.6	c.716-7156T>G		intron_variant		5	NM_015589.6	ENSP00000452535.1

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

Gnomad4 AFR AF: 0.423

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.340

Gnomad4 OTH AF: 0.330

Alfa AF: 0.339 Hom.: 4408

Bravo AF: 0.349

Asia WGS AF: 0.306 AC: 1060 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	13
DANN	Benign	0.61

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: rs4898848; hg19: chr14-55196586;