ENST00000625758.3:n.1320+56842T>C

Variant names:

• chr8-118821226-T-C
• rs1389545
• ENST00000625758.3:n.1320+56842T>C

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+56842T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.811 in 142,742 control chromosomes in the GnomAD database, including 44,611 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 0.81 (44611 hom., cov: 30)
• Consequence: SAMD12-AS1 ENST00000625758.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 2 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.876 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+56842T>C		intron	N/A
	SAMD12-AS1	ENST00000629661.1	TSL:5	n.496-36831T>C		intron	N/A
	SAMD12-AS1	ENST00000658340.1		n.900+56842T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.810 AC: 115602 AN: 142634 Hom.: 44554 Cov.: 30

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.634

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.744

Gnomad MID AF: 0.707

Gnomad NFE AF: 0.806

Gnomad OTH AF: 0.796

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

GnomAD4 genome AF: 0.811 AC: 115713 AN: 142742 Hom.: 44611 Cov.: 30 AF XY: 0.804 AC XY: 55750 AN XY: 69302

African (AFR) AF: 0.883 AC: 35984 AN: 40738

American (AMR) AF: 0.767 AC: 10719 AN: 13968

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2201 AN: 3008

East Asian (EAS) AF: 0.634 AC: 2797 AN: 4414

South Asian (SAS) AF: 0.723 AC: 2939 AN: 4066

European-Finnish (FIN) AF: 0.744 AC: 6966 AN: 9364

Middle Eastern (MID) AF: 0.702 AC: 174 AN: 248

European-Non Finnish (NFE) AF: 0.806 AC: 51641 AN: 64108

Other (OTH) AF: 0.796 AC: 1544 AN: 1940

Alfa AF: 0.604 Hom.: 771

Bravo AF: 0.768

Asia WGS AF: 0.620 AC: 1978 AN: 3184

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.66
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1389545; hg19: chr8-119833465;