rs6469756

chr8-118544191-A-Gchr8-118544191-A-T

Variant summary

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

The NM_207506.3(SAMD12):c.192+36524T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.81 in 152,168 control chromosomes in the GnomAD database, including 50,492 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 0.81 (50492 hom., cov: 32)
• Consequence: SAMD12 NM_207506.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.127

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SAMD12	NM_207506.3	c.192+36524T>C		intron_variant		ENST00000314727.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SAMD12	ENST00000314727.9	c.192+36524T>C		intron_variant		1	NM_207506.3

Frequencies

GnomAD3 genomes AF: 0.810 AC: 123192 AN: 152050 Hom.: 50431 Cov.: 32

Gnomad AFR AF: 0.909

Gnomad AMI AF: 0.718

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.791

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.810 AC: 123313 AN: 152168 Hom.: 50492 Cov.: 32 AF XY: 0.809 AC XY: 60180 AN XY: 74370

Gnomad4 AFR AF: 0.909

Gnomad4 AMR AF: 0.831

Gnomad4 ASJ AF: 0.744

Gnomad4 EAS AF: 0.541

Gnomad4 SAS AF: 0.797

Gnomad4 FIN AF: 0.791

Gnomad4 NFE AF: 0.776

Gnomad4 OTH AF: 0.777

Alfa AF: 0.782 Hom.: 46004

Bravo AF: 0.817

Asia WGS AF: 0.670 AC: 2331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.9
Dann	Benign	0.41

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: rs6469756; hg19: chr8-119556430;