8-118810334-T-A

Variant names:

• chr8-118810334-T-A
• rs12545372
• ENST00000625758.3:n.1320+45950T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000658340.1(SAMD12-AS1):​n.900+45950T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 152,044 control chromosomes in the GnomAD database, including 14,854 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 0.40 (14854 hom., cov: 32)
• Consequence: SAMD12-AS1 ENST00000658340.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.394
• Publications: 4 publications found

Genes affected

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

ENSG00000306504 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658340.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAMD12-AS1	ENST00000625758.3	TSL:5	n.1320+45950T>A		intron	N/A
	SAMD12-AS1	ENST00000629661.1	TSL:5	n.496-47723T>A		intron	N/A
	SAMD12-AS1	ENST00000658340.1		n.900+45950T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60780 AN: 151926 Hom.: 14851 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.400 AC: 60790 AN: 152044 Hom.: 14854 Cov.: 32 AF XY: 0.391 AC XY: 29033 AN XY: 74316

African (AFR) AF: 0.137 AC: 5690 AN: 41500

American (AMR) AF: 0.426 AC: 6510 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1579 AN: 3468

East Asian (EAS) AF: 0.132 AC: 686 AN: 5180

South Asian (SAS) AF: 0.275 AC: 1327 AN: 4824

European-Finnish (FIN) AF: 0.477 AC: 5041 AN: 10562

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.564 AC: 38308 AN: 67930

Other (OTH) AF: 0.429 AC: 905 AN: 2108

Alfa AF: 0.357 Hom.: 1165

Bravo AF: 0.388

Asia WGS AF: 0.213 AC: 743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.8
DANN	Benign	0.77
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs12545372; hg19: chr8-119822573;