NM_001258275.3:c.-187-6105G>T

Variant names:

• chr6-130228918-C-A
• rs10447419
• NM_001258275.3:c.-187-6105G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001258275.3(SAMD3):​c.-187-6105G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152,124 control chromosomes in the GnomAD database, including 5,221 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 0.25 (5221 hom., cov: 32)
• Consequence: SAMD3 NM_001258275.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810
• Publications: 12 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001258275.3. 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_001258275.3		c.-187-6105G>T		intron	N/A	NP_001245204.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAMD3	ENST00000368134.6	TSL:2	c.-187-6105G>T		intron	N/A	ENSP00000357116.2
	SAMD3	ENST00000529119.1	TSL:3	n.70-6105G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37383 AN: 152004 Hom.: 5207 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.246 AC: 37429 AN: 152124 Hom.: 5221 Cov.: 32 AF XY: 0.255 AC XY: 18973 AN XY: 74356

African (AFR) AF: 0.153 AC: 6369 AN: 41536

American (AMR) AF: 0.362 AC: 5533 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1035 AN: 3472

East Asian (EAS) AF: 0.471 AC: 2431 AN: 5158

South Asian (SAS) AF: 0.371 AC: 1789 AN: 4818

European-Finnish (FIN) AF: 0.296 AC: 3132 AN: 10574

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16285 AN: 67968

Other (OTH) AF: 0.253 AC: 534 AN: 2112

Alfa AF: 0.221 Hom.: 1731

Bravo AF: 0.245

Asia WGS AF: 0.467 AC: 1625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.60
PhyloP100		-0.081
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: rs10447419; hg19: chr6-130550063;