rs10505328

chr8-118138219-G-Achr8-118138219-G-Cchr8-118138219-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, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.219

Genes affected

SAMD12 (HGNC:):

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/exons	MANE	UniProt
SAMD12	NR_146234.2	n.703-5662C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;