rs10505328

Variant names:

• chr8-118138219-G-A
• rs10505328
• NR_146234.2:n.703-5662C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-118138219-G-A
• chr8-118138219-G-C
• chr8-118138219-G-T

Variant summary

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

The NR_146234.2(SAMD12):​n.703-5662C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 151,970 control chromosomes in the GnomAD database, including 12,861 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 0.39 (12861 hom., cov: 32)
• Consequence: SAMD12 NR_146234.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.219

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SAMD12	NR_146234.2	n.703-5662C>T		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59021 AN: 151850 Hom.: 12861 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.389 AC: 59041 AN: 151970 Hom.: 12861 Cov.: 32 AF XY: 0.389 AC XY: 28854 AN XY: 74256

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.513

Gnomad4 EAS AF: 0.496

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.497

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.402

Alfa AF: 0.437 Hom.: 8602

Bravo AF: 0.373

Asia WGS AF: 0.372 AC: 1297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.27
DANN	Benign	0.64

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10505328; hg19: chr8-119150458;