chr8-118810334-T-A

Position:

• chr8-118810334-T-A

Variant summary

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

The ENST00000625758.3(SAMD12-AS1):​n.1320+45950T>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 152,044 control chromosomes in the GnomAD database, including 14,854 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 0.40 (14854 hom., cov: 32)
• Consequence: SAMD12-AS1 ENST00000625758.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.394

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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SAMD12-AS1	ENST00000625758.3	n.1320+45950T>A		intron_variant, non_coding_transcript_variant		5
SAMD12-AS1	ENST00000629661.1	n.496-47723T>A		intron_variant, non_coding_transcript_variant		5
SAMD12-AS1	ENST00000658340.1	n.900+45950T>A		intron_variant, non_coding_transcript_variant
SAMD12-AS1	ENST00000664584.1	n.760+45950T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60780 AN: 151926 Hom.: 14851 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.400 AC: 60790 AN: 152044 Hom.: 14854 Cov.: 32 AF XY: 0.391 AC XY: 29033 AN XY: 74316

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.455

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.477

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.429

Alfa AF: 0.357 Hom.: 1165

Bravo AF: 0.388

Asia WGS AF: 0.213 AC: 743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.8
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12545372; hg19: chr8-119822573;