rs17749211

Variant names:

• chr8-118379170-C-A
• rs17749211
• NM_207506.3:c.*247G>T

Your query was ambiguous. Multiple possible variants found:

• chr8-118379170-C-A
• chr8-118379170-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_207506.3(SAMD12):​c.*247G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000279 in 1,075,446 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0000028 (0 hom.)
• Consequence: SAMD12 NM_207506.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 7 publications found

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 Gene-Disease associations (from GenCC):

• epilepsy, familial adult myoclonic, 1

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• benign adult familial myoclonic epilepsy

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ENSG00000225885 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SAMD12	NM_207506.3	c.*247G>T		3_prime_UTR_variant	Exon 4 of 4	ENST00000314727.9	NP_997389.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SAMD12	ENST00000314727.9	c.*247G>T		3_prime_UTR_variant	Exon 4 of 4	1	NM_207506.3	ENSP00000314173.4

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000279 AC: 3 AN: 1075446 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 508276

African (AFR) AF: 0.00 AC: 0 AN: 24654

American (AMR) AF: 0.00 AC: 0 AN: 11140

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13760

East Asian (EAS) AF: 0.00 AC: 0 AN: 26080

South Asian (SAS) AF: 0.0000380 AC: 1 AN: 26302

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 15652

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2798

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 912206

Other (OTH) AF: 0.0000467 AC: 2 AN: 42854

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 644

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.059
DANN	Benign	0.57
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism

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: rs17749211; hg19: chr8-119391409;