8-118244617-G-A

Position:

• chr8-118244617-G-A

Variant summary

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

The NM_001101676.2(SAMD12):​c.464-46885C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 151,742 control chromosomes in the GnomAD database, including 2,076 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 0.14 (2076 hom., cov: 32)
• Consequence: SAMD12 NM_001101676.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SAMD12	NM_001101676.2	c.464-46885C>T		intron_variant			NP_001095146.1
SAMD12	NM_001349811.2	c.434-46885C>T		intron_variant			NP_001336740.1
SAMD12	XM_047421779.1	c.464-3347C>T		intron_variant			XP_047277735.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SAMD12	ENST00000524796.6	c.464-46885C>T		intron_variant		3		ENSP00000435927.2
SAMD12	ENST00000409003.5	c.434-46885C>T		intron_variant		5		ENSP00000387133.5
SAMD12	ENST00000445741.6	n.*127-4642C>T		intron_variant		3		ENSP00000387605.1
SAMD12	ENST00000453675.7	n.172-3347C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21063 AN: 151624 Hom.: 2069 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0548

Gnomad EAS AF: 0.0952

Gnomad SAS AF: 0.0372

Gnomad FIN AF: 0.0718

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0849

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.139 AC: 21090 AN: 151742 Hom.: 2076 Cov.: 32 AF XY: 0.135 AC XY: 10042 AN XY: 74124

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.0548

Gnomad4 EAS AF: 0.0956

Gnomad4 SAS AF: 0.0375

Gnomad4 FIN AF: 0.0718

Gnomad4 NFE AF: 0.0850

Gnomad4 OTH AF: 0.127

Alfa AF: 0.104 Hom.: 406

Bravo AF: 0.150

Asia WGS AF: 0.0730 AC: 254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.4
DANN	Benign	0.58

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: rs17455085; hg19: chr8-119256856;