rs3103986

Positions:

• chr8-118795983-C-T

Variant summary

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

The ENST00000625758.3(SAMD12-AS1):​n.1320+31599C>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 0.358 in 151,870 control chromosomes in the GnomAD database, including 10,871 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 0.36 (10871 hom., cov: 32)
• Consequence: SAMD12-AS1 ENST00000625758.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238

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 (NFE) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SAMD12-AS1	ENST00000625758.3	n.1320+31599C>T		intron_variant, non_coding_transcript_variant		5
SAMD12-AS1	ENST00000629661.1	n.496-62074C>T		intron_variant, non_coding_transcript_variant		5
SAMD12-AS1	ENST00000658340.1	n.900+31599C>T		intron_variant, non_coding_transcript_variant
SAMD12-AS1	ENST00000664584.1	n.760+31599C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54342 AN: 151752 Hom.: 10865 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.358 AC: 54362 AN: 151870 Hom.: 10871 Cov.: 32 AF XY: 0.354 AC XY: 26259 AN XY: 74230

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.378

Alfa AF: 0.413 Hom.: 1723

Bravo AF: 0.350

Asia WGS AF: 0.189 AC: 659 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.8
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3103986; hg19: chr8-119808222;