rs769322

chr8-118657129-A-G

Variant summary

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

The NR_038210.1(SAMD12-AS1):n.308-11321A>G 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 0.496 in 152,120 control chromosomes in the GnomAD database, including 22,147 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 0.50 (22147 hom., cov: 33)
• Consequence: SAMD12-AS1 NR_038210.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SAMD12-AS1	NR_038210.1	n.308-11321A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SAMD12-AS1	ENST00000625758.3	n.811-11321A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75475 AN: 152002 Hom.: 22147 Cov.: 33

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.496 AC: 75478 AN: 152120 Hom.: 22147 Cov.: 33 AF XY: 0.501 AC XY: 37259 AN XY: 74332

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.634

Gnomad4 ASJ AF: 0.559

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.696

Gnomad4 NFE AF: 0.634

Gnomad4 OTH AF: 0.540

Alfa AF: 0.600 Hom.: 12937

Bravo AF: 0.478

Asia WGS AF: 0.366 AC: 1276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	5.2
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: rs769322; hg19: chr8-119669368;