8-118747329-C-T

Position:

• chr8-118747329-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.311

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.118747329C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SAMD12-AS1	ENST00000625758.3	n.1205-16940C>T		intron_variant		5
SAMD12-AS1	ENST00000629661.1	n.495+21262C>T		intron_variant		5
SAMD12-AS1	ENST00000658340.1	n.785-16940C>T		intron_variant

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

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.628

Gnomad4 ASJ AF: 0.567

Gnomad4 EAS AF: 0.403

Gnomad4 SAS AF: 0.513

Gnomad4 FIN AF: 0.661

Gnomad4 NFE AF: 0.708

Gnomad4 OTH AF: 0.591

Alfa AF: 0.641 Hom.: 4045

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1160273; hg19: chr8-119759568;