rs10447419

Positions:

• chr6-130228918-C-A
• chr6-130228918-C-G
• chr6-130228918-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

SAMD3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SAMD3	NM_001258275.3	c.-187-6105G>T		intron_variant			NP_001245204.1
SAMD3	XM_024446335.2	c.-187-6105G>T		intron_variant			XP_024302103.1
SAMD3	XM_047418239.1	c.-67-12302G>T		intron_variant			XP_047274195.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SAMD3	ENST00000368134.6	c.-187-6105G>T		intron_variant		2		ENSP00000357116.2
SAMD3	ENST00000529119.1	n.70-6105G>T		intron_variant		3

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

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.371

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.253

Alfa AF: 0.209 Hom.: 1076

Bravo AF: 0.245

Asia WGS AF: 0.467 AC: 1625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.60

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: rs10447419; hg19: chr6-130550063;