chr14-54620115-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015589.6(SAMD4A):​c.196+52003A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 151,726 control chromosomes in the GnomAD database, including 22,238 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 ( 22238 hom., cov: 30)

Consequence

SAMD4A
NM_015589.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0360
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
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 Protein UniProt
SAMD4ANM_015589.6 linkuse as main transcriptc.196+52003A>G intron_variant ENST00000554335.6 NP_056404.4
LOC112268133XR_002957606.2 linkuse as main transcriptn.11010A>G non_coding_transcript_exon_variant 2/2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SAMD4AENST00000554335.6 linkuse as main transcriptc.196+52003A>G intron_variant 5 NM_015589.6 ENSP00000452535 A1Q9UPU9-1

Frequencies

GnomAD3 genomes
AF:
0.537
AC:
81389
AN:
151610
Hom.:
22239
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.492
Gnomad AMI
AF:
0.523
Gnomad AMR
AF:
0.550
Gnomad ASJ
AF:
0.456
Gnomad EAS
AF:
0.870
Gnomad SAS
AF:
0.559
Gnomad FIN
AF:
0.628
Gnomad MID
AF:
0.544
Gnomad NFE
AF:
0.524
Gnomad OTH
AF:
0.539
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.537
AC:
81426
AN:
151726
Hom.:
22238
Cov.:
30
AF XY:
0.544
AC XY:
40371
AN XY:
74146
show subpopulations
Gnomad4 AFR
AF:
0.492
Gnomad4 AMR
AF:
0.549
Gnomad4 ASJ
AF:
0.456
Gnomad4 EAS
AF:
0.870
Gnomad4 SAS
AF:
0.560
Gnomad4 FIN
AF:
0.628
Gnomad4 NFE
AF:
0.524
Gnomad4 OTH
AF:
0.538
Alfa
AF:
0.528
Hom.:
25250
Bravo
AF:
0.531
Asia WGS
AF:
0.646
AC:
2245
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
1.4
DANN
Benign
0.64

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9285581; hg19: chr14-55086833; API