ENST00000625758.3:n.1320+18616A>G

Variant names:

• chr8-118783000-A-G
• rs1493941
• ENST00000625758.3:n.1320+18616A>G

Variant summary

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

The ENST00000625758.3(SAMD12-AS1):​n.1320+18616A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 151,956 control chromosomes in the GnomAD database, including 20,978 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 0.50 (20978 hom., cov: 31)
• Consequence: SAMD12-AS1 ENST00000625758.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 1 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.712 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000625758.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAMD12-AS1	ENST00000625758.3	TSL:5	n.1320+18616A>G		intron	N/A
	SAMD12-AS1	ENST00000629661.1	TSL:5	n.495+56933A>G		intron	N/A
	SAMD12-AS1	ENST00000658340.1		n.900+18616A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76318 AN: 151838 Hom.: 20956 Cov.: 31

Gnomad AFR AF: 0.718

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.503 AC: 76391 AN: 151956 Hom.: 20978 Cov.: 31 AF XY: 0.502 AC XY: 37244 AN XY: 74252

African (AFR) AF: 0.718 AC: 29787 AN: 41464

American (AMR) AF: 0.490 AC: 7485 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1724 AN: 3472

East Asian (EAS) AF: 0.686 AC: 3517 AN: 5130

South Asian (SAS) AF: 0.591 AC: 2849 AN: 4820

European-Finnish (FIN) AF: 0.317 AC: 3351 AN: 10564

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26283 AN: 67926

Other (OTH) AF: 0.477 AC: 1010 AN: 2116

Alfa AF: 0.449 Hom.: 2221

Bravo AF: 0.522

Asia WGS AF: 0.607 AC: 2108 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.8
DANN	Benign	0.43
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs1493941; hg19: chr8-119795239;