rs1402513

Variant names:

• chr8-118647940-C-T
• rs1402513
• ENST00000625758.3:n.811-20510C>T

Variant summary

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

The NR_038210.1(SAMD12-AS1):​n.308-20510C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 152,018 control chromosomes in the GnomAD database, including 22,043 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 0.49 (22043 hom., cov: 31)
• Consequence: SAMD12-AS1 NR_038210.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.500

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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SAMD12-AS1	NR_038210.1	n.308-20510C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SAMD12-AS1	ENST00000625758.3	n.811-20510C>T		intron_variant	Intron 2 of 7	5
SAMD12-AS1	ENST00000629661.1	n.102-20510C>T		intron_variant	Intron 1 of 4	5
SAMD12-AS1	ENST00000658340.1	n.263-20510C>T		intron_variant	Intron 1 of 7

Frequencies

GnomAD3 genomes AF: 0.494 AC: 75056 AN: 151902 Hom.: 22044 Cov.: 31

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.494 AC: 75058 AN: 152018 Hom.: 22043 Cov.: 31 AF XY: 0.499 AC XY: 37059 AN XY: 74298

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.632

Gnomad4 ASJ AF: 0.558

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.697

Gnomad4 NFE AF: 0.634

Gnomad4 OTH AF: 0.538

Alfa AF: 0.617 Hom.: 38984

Bravo AF: 0.475

Asia WGS AF: 0.365 AC: 1273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.4
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1402513; hg19: chr8-119660179;