rs3103986

Variant names:

• chr8-118795983-C-T
• rs3103986
• ENST00000625758.3:n.1320+31599C>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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SAMD12-AS1	ENST00000625758.3	n.1320+31599C>T		intron_variant	Intron 6 of 7	5
SAMD12-AS1	ENST00000629661.1	n.496-62074C>T		intron_variant	Intron 4 of 4	5
SAMD12-AS1	ENST00000658340.1	n.900+31599C>T		intron_variant	Intron 6 of 7
SAMD12-AS1	ENST00000664584.1	n.760+31599C>T		intron_variant	Intron 5 of 6

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;