ENST00000625758.3:n.1205-16940C>T

Variant names:

• chr8-118747329-C-T
• rs1160273
• ENST00000625758.3:n.1205-16940C>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.1205-16940C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 151,884 control chromosomes in the GnomAD database, including 27,128 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 0.58 (27128 hom., cov: 31)
• Consequence: SAMD12-AS1 ENST00000625758.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.311
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SAMD12-AS1	ENST00000625758.3	n.1205-16940C>T		intron_variant	Intron 5 of 7	5
SAMD12-AS1	ENST00000629661.1	n.495+21262C>T		intron_variant	Intron 4 of 4	5
SAMD12-AS1	ENST00000658340.1	n.785-16940C>T		intron_variant	Intron 5 of 7

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87442 AN: 151764 Hom.: 27114 Cov.: 31

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.576 AC: 87484 AN: 151884 Hom.: 27128 Cov.: 31 AF XY: 0.572 AC XY: 42426 AN XY: 74224

African (AFR) AF: 0.345 AC: 14297 AN: 41412

American (AMR) AF: 0.628 AC: 9576 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 1968 AN: 3468

East Asian (EAS) AF: 0.403 AC: 2073 AN: 5140

South Asian (SAS) AF: 0.513 AC: 2476 AN: 4822

European-Finnish (FIN) AF: 0.661 AC: 6955 AN: 10528

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.708 AC: 48089 AN: 67944

Other (OTH) AF: 0.591 AC: 1246 AN: 2108

Alfa AF: 0.623 Hom.: 9091

Bravo AF: 0.564

Asia WGS AF: 0.462 AC: 1609 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.6
DANN	Benign	0.72
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs1160273; hg19: chr8-119759568;