8-118710824-C-T

Variant names:

• chr8-118710824-C-T
• rs7816831
• ENST00000625758.3:n.963-13695C>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.963-13695C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 151,884 control chromosomes in the GnomAD database, including 23,644 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 0.53 (23644 hom., cov: 32)
• Consequence: SAMD12-AS1 ENST00000625758.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.216
• Publications: 2 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SAMD12-AS1	NR_038210.1	n.460-13695C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SAMD12-AS1	ENST00000625758.3	n.963-13695C>T		intron_variant	Intron 3 of 7	5
SAMD12-AS1	ENST00000629661.1	n.254-13695C>T		intron_variant	Intron 2 of 4	5
SAMD12-AS1	ENST00000658340.1	n.543-13695C>T		intron_variant	Intron 3 of 7

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79745 AN: 151766 Hom.: 23578 Cov.: 32

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.526 AC: 79862 AN: 151884 Hom.: 23644 Cov.: 32 AF XY: 0.517 AC XY: 38345 AN XY: 74190

African (AFR) AF: 0.811 AC: 33614 AN: 41452

American (AMR) AF: 0.448 AC: 6837 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1318 AN: 3470

East Asian (EAS) AF: 0.170 AC: 878 AN: 5156

South Asian (SAS) AF: 0.323 AC: 1553 AN: 4804

European-Finnish (FIN) AF: 0.409 AC: 4291 AN: 10496

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29820 AN: 67940

Other (OTH) AF: 0.477 AC: 1007 AN: 2110

Alfa AF: 0.393 Hom.: 1804

Bravo AF: 0.541

Asia WGS AF: 0.312 AC: 1087 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.58
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs7816831; hg19: chr8-119723063;