rs1402513

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_038210.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAMD12-AS1	NR_038210.1		n.308-20510C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAMD12-AS1	ENST00000625758.3	TSL:5	n.811-20510C>T		intron	N/A
	SAMD12-AS1	ENST00000629661.1	TSL:5	n.102-20510C>T		intron	N/A
	SAMD12-AS1	ENST00000658340.1		n.263-20510C>T		intron	N/A

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

African (AFR) AF: 0.169 AC: 7015 AN: 41482

American (AMR) AF: 0.632 AC: 9652 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1935 AN: 3466

East Asian (EAS) AF: 0.316 AC: 1633 AN: 5170

South Asian (SAS) AF: 0.535 AC: 2580 AN: 4824

European-Finnish (FIN) AF: 0.697 AC: 7350 AN: 10552

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.634 AC: 43056 AN: 67948

Other (OTH) AF: 0.538 AC: 1137 AN: 2112

Alfa AF: 0.603 Hom.: 47722

Bravo AF: 0.475

Asia WGS AF: 0.365 AC: 1273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.4
DANN	Benign	0.71
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs1402513; hg19: chr8-119660179;