8-118483688-C-T

Position:

• chr8-118483688-C-T

Variant summary

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

The NM_207506.3(SAMD12):​c.193-43727G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.939 in 152,292 control chromosomes in the GnomAD database, including 67,230 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 0.94 (67230 hom., cov: 32)
• Consequence: SAMD12 NM_207506.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27

Genes affected

SAMD12 (HGNC:31750): (sterile alpha motif domain containing 12) Predicted to be involved in transmembrane receptor protein tyrosine kinase signaling pathway. Predicted to be active in cytoplasmic side of plasma membrane. Implicated in familial adult myoclonic epilepsy 1. [provided by Alliance of Genome Resources, Apr 2022]

SAMD12 (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 (AFR) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SAMD12	NM_207506.3	c.193-43727G>A		intron_variant		ENST00000314727.9	NP_997389.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SAMD12	ENST00000314727.9	c.193-43727G>A		intron_variant		1	NM_207506.3	ENSP00000314173.4

Frequencies

GnomAD3 genomes AF: 0.939 AC: 142901 AN: 152174 Hom.: 67180 Cov.: 32

Gnomad AFR AF: 0.954

Gnomad AMI AF: 0.995

Gnomad AMR AF: 0.953

Gnomad ASJ AF: 0.919

Gnomad EAS AF: 0.804

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.966

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.940

Gnomad OTH AF: 0.930

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

GnomAD4 genome AF: 0.939 AC: 143009 AN: 152292 Hom.: 67230 Cov.: 32 AF XY: 0.939 AC XY: 69893 AN XY: 74460

Gnomad4 AFR AF: 0.954

Gnomad4 AMR AF: 0.953

Gnomad4 ASJ AF: 0.919

Gnomad4 EAS AF: 0.805

Gnomad4 SAS AF: 0.837

Gnomad4 FIN AF: 0.966

Gnomad4 NFE AF: 0.940

Gnomad4 OTH AF: 0.929

Alfa AF: 0.934 Hom.: 32425

Bravo AF: 0.941

Asia WGS AF: 0.804 AC: 2800 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	0.015
DANN	Benign	0.57

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: rs2515034; hg19: chr8-119495927;