rs11154532

Variant names:

• chr6-130204230-T-C
• rs11154532
• NM_001017373.4:c.383+5265A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001017373.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAMD3	NM_001017373.4	MANE Select	c.383+5265A>G		intron	N/A	NP_001017373.2
	SAMD3	NM_001277185.2		c.455+5265A>G		intron	N/A	NP_001264114.1
	SAMD3	NM_001258275.3		c.383+5265A>G		intron	N/A	NP_001245204.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAMD3	ENST00000439090.7	TSL:2 MANE Select	c.383+5265A>G		intron	N/A	ENSP00000403565.2
	SAMD3	ENST00000324172.10	TSL:1	c.383+5265A>G		intron	N/A	ENSP00000324874.6
	SAMD3	ENST00000524930.1	TSL:1	n.*267+5265A>G		intron	N/A	ENSP00000436997.1

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

African (AFR) AF: 0.0859 AC: 3565 AN: 41522

American (AMR) AF: 0.342 AC: 5230 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 857 AN: 3470

East Asian (EAS) AF: 0.440 AC: 2267 AN: 5158

South Asian (SAS) AF: 0.208 AC: 999 AN: 4802

European-Finnish (FIN) AF: 0.277 AC: 2925 AN: 10554

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15719 AN: 67992

Other (OTH) AF: 0.208 AC: 439 AN: 2112

Alfa AF: 0.239 Hom.: 873

Bravo AF: 0.214

Asia WGS AF: 0.331 AC: 1150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.0
DANN	Benign	0.67
PhyloP100		0.15
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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