rs10505337

Positions:

• chr8-118754926-G-A
• chr8-118754926-G-T

Variant summary

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

The ENST00000625758.3(SAMD12-AS1):​n.1205-9343G>A 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 0.583 in 151,898 control chromosomes in the GnomAD database, including 27,529 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 0.58 (27529 hom., cov: 32)
• Consequence: SAMD12-AS1 ENST00000625758.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.188

Genes affected

SAMD12-AS1 (HGNC:30937): (SAMD12 antisense RNA 1)

LOC124902007 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902007	XR_007061074.1	n.86-998C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SAMD12-AS1	ENST00000625758.3	n.1205-9343G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88531 AN: 151780 Hom.: 27514 Cov.: 32

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.583 AC: 88574 AN: 151898 Hom.: 27529 Cov.: 32 AF XY: 0.579 AC XY: 42946 AN XY: 74226

Gnomad4 AFR AF: 0.370

Gnomad4 AMR AF: 0.629

Gnomad4 ASJ AF: 0.568

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.661

Gnomad4 NFE AF: 0.708

Gnomad4 OTH AF: 0.596

Alfa AF: 0.663 Hom.: 18744

Bravo AF: 0.571

Asia WGS AF: 0.467 AC: 1628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.94
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10505337; hg19: chr8-119767165;