chr14-54620150-C-T

Position:

• chr14-54620150-C-T

Variant summary

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

The NM_015589.6(SAMD4A):​c.196+52038C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 151,692 control chromosomes in the GnomAD database, including 22,186 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 (22186 hom., cov: 30)
• Consequence: SAMD4A NM_015589.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290

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=-0.91).
• 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/exons	MANE	UniProt
SAMD4A	NM_015589.6	c.196+52038C>T		intron_variant		ENST00000554335.6
LOC112268133	XR_002957606.2	n.11045C>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SAMD4A	ENST00000554335.6	c.196+52038C>T		intron_variant		5	NM_015589.6	A1

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81256 AN: 151578 Hom.: 22187 Cov.: 30

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.536 AC: 81292 AN: 151692 Hom.: 22186 Cov.: 30 AF XY: 0.544 AC XY: 40280 AN XY: 74100

Gnomad4 AFR AF: 0.491

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.870

Gnomad4 SAS AF: 0.556

Gnomad4 FIN AF: 0.629

Gnomad4 NFE AF: 0.523

Gnomad4 OTH AF: 0.540

Alfa AF: 0.528 Hom.: 2655

Bravo AF: 0.530

Asia WGS AF: 0.644 AC: 2239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.47

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: rs9285582; hg19: chr14-55086868;