rs7814509

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

SAMD12-AS1 (HGNC:30937): (SAMD12 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -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.

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.1320+16622C>T		intron_variant	Intron 6 of 7	5
SAMD12-AS1	ENST00000629661.1	n.495+54939C>T		intron_variant	Intron 4 of 4	5
SAMD12-AS1	ENST00000658340.1	n.900+16622C>T		intron_variant	Intron 6 of 7

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

Gnomad4 AFR AF: 0.744

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.685

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.482

Alfa AF: 0.442 Hom.: 2066

Bravo AF: 0.530

Asia WGS AF: 0.606 AC: 2105 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7814509; hg19: chr8-119793245;