ENST00000625758.3:n.1320+16622C>T

Variant names:

• chr8-118781006-C-T
• rs7814509
• ENST00000625758.3:n.1320+16622C>T

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+16622C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 151,892 control chromosomes in the GnomAD database, including 21,788 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 0.51 (21788 hom., cov: 32)
• Consequence: SAMD12-AS1 ENST00000625758.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.977
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.737 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAMD12-AS1	ENST00000625758.3	TSL:5	n.1320+16622C>T		intron	N/A
	SAMD12-AS1	ENST00000629661.1	TSL:5	n.495+54939C>T		intron	N/A
	SAMD12-AS1	ENST00000658340.1		n.900+16622C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77315 AN: 151774 Hom.: 21773 Cov.: 32

Gnomad AFR AF: 0.745

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.509 AC: 77380 AN: 151892 Hom.: 21788 Cov.: 32 AF XY: 0.507 AC XY: 37665 AN XY: 74228

African (AFR) AF: 0.744 AC: 30860 AN: 41458

American (AMR) AF: 0.490 AC: 7472 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1718 AN: 3472

East Asian (EAS) AF: 0.685 AC: 3535 AN: 5160

South Asian (SAS) AF: 0.590 AC: 2840 AN: 4814

European-Finnish (FIN) AF: 0.318 AC: 3347 AN: 10530

Middle Eastern (MID) AF: 0.428 AC: 125 AN: 292

European-Non Finnish (NFE) AF: 0.386 AC: 26205 AN: 67896

Other (OTH) AF: 0.482 AC: 1019 AN: 2114

Alfa AF: 0.453 Hom.: 2283

Bravo AF: 0.530

Asia WGS AF: 0.606 AC: 2105 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.57
DANN	Benign	0.63
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs7814509; hg19: chr8-119793245;