8-118379170-C-T

Position:

• chr8-118379170-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.*247G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0597 in 1,227,446 control chromosomes in the GnomAD database, including 2,789 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 0.054 (482 hom., cov: 33)
  • Exomes 𝑓: 0.061 (2307 hom.)
• Consequence: SAMD12 NM_207506.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SAMD12	NM_207506.3	c.*247G>A		3_prime_UTR_variant	4/4	ENST00000314727.9	NP_997389.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SAMD12	ENST00000314727.9	c.*247G>A		3_prime_UTR_variant	4/4	1	NM_207506.3	ENSP00000314173.4

Frequencies

GnomAD3 genomes AF: 0.0538 AC: 8181 AN: 152126 Hom.: 480 Cov.: 33

Gnomad AFR AF: 0.0127

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.0421

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0300

Gnomad FIN AF: 0.0368

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0584

Gnomad OTH AF: 0.0583

GnomAD4 exome AF: 0.0606 AC: 65119 AN: 1075202 Hom.: 2307 Cov.: 30 AF XY: 0.0605 AC XY: 30720 AN XY: 508158

Gnomad4 AFR exome AF: 0.00840

Gnomad4 AMR exome AF: 0.201

Gnomad4 ASJ exome AF: 0.0419

Gnomad4 EAS exome AF: 0.000460

Gnomad4 SAS exome AF: 0.0359

Gnomad4 FIN exome AF: 0.0403

Gnomad4 NFE exome AF: 0.0637

Gnomad4 OTH exome AF: 0.0552

GnomAD4 genome AF: 0.0538 AC: 8187 AN: 152244 Hom.: 482 Cov.: 33 AF XY: 0.0550 AC XY: 4097 AN XY: 74432

Gnomad4 AFR AF: 0.0126

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.0421

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0302

Gnomad4 FIN AF: 0.0368

Gnomad4 NFE AF: 0.0584

Gnomad4 OTH AF: 0.0577

Alfa AF: 0.0559 Hom.: 451

Bravo AF: 0.0625

Asia WGS AF: 0.0200 AC: 72 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.27
DANN	Benign	0.71

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: rs17749211; hg19: chr8-119391409;