rs11154532

chr6-130204230-T-C

Variant summary

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

The NM_001017373.4(SAMD3):c.383+5265A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,088 control chromosomes in the GnomAD database, including 4,232 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 0.21 (4232 hom., cov: 32)
• Consequence: SAMD3 NM_001017373.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146

Genes affected

SAMD3 (HGNC:21574): (sterile alpha motif domain containing 3)

ACMG classification

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 = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SAMD3	NM_001017373.4	c.383+5265A>G		intron_variant		ENST00000439090.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SAMD3	ENST00000439090.7	c.383+5265A>G		intron_variant		2	NM_001017373.4	P1

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32266 AN: 151970 Hom.: 4229 Cov.: 32

Gnomad AFR AF: 0.0857

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.212 AC: 32277 AN: 152088 Hom.: 4232 Cov.: 32 AF XY: 0.219 AC XY: 16288 AN XY: 74320

Gnomad4 AFR AF: 0.0859

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.440

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.208

Alfa AF: 0.243 Hom.: 870

Bravo AF: 0.214

Asia WGS AF: 0.331 AC: 1150 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	7.0
Dann	Benign	0.67

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: rs11154532; hg19: chr6-130525375; COSMIC: COSV60774917;