rs562638

Positions:

• chr19-39359149-A-G

Variant summary

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

The NM_001384574.2(SAMD4B):​c.196+2060A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 152,078 control chromosomes in the GnomAD database, including 11,743 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 0.28 (11743 hom., cov: 32)
• Consequence: SAMD4B NM_001384574.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

Genes affected

SAMD4B (HGNC:25492): (sterile alpha motif domain containing 4B) Enables RNA binding activity. Predicted to be involved in nuclear-transcribed mRNA poly(A) tail shortening. Predicted to act upstream of or within cerebellar neuron development. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SAMD4B	NM_001384574.2	c.196+2060A>G		intron_variant		ENST00000610417.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SAMD4B	ENST00000610417.5	c.196+2060A>G		intron_variant		2	NM_001384574.2	P1

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42843 AN: 151960 Hom.: 11688 Cov.: 32

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.0832

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.147

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.282 AC: 42952 AN: 152078 Hom.: 11743 Cov.: 32 AF XY: 0.276 AC XY: 20501 AN XY: 74342

Gnomad4 AFR AF: 0.721

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.0830

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.249

Alfa AF: 0.185 Hom.: 2072

Bravo AF: 0.307

Asia WGS AF: 0.153 AC: 535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.056
DANN	Benign	0.32

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: rs562638; hg19: chr19-39849789;