rs1090502

Positions:

• chr3-70345072-A-G

Variant summary

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

The ENST00000642114.1(SAMMSON):​n.740-9103A>G 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 0.135 in 152,214 control chromosomes in the GnomAD database, including 1,497 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 0.14 (1497 hom., cov: 32)
• Consequence: SAMMSON ENST00000642114.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263

Genes affected

SAMMSON (HGNC:49644): (survival associated mitochondrial melanoma specific oncogenic non-coding RNA)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SAMMSON	ENST00000642114.1	n.740-9103A>G		intron_variant, non_coding_transcript_variant
SAMMSON	ENST00000641053.1	n.162+12171A>G		intron_variant, non_coding_transcript_variant
SAMMSON	ENST00000641222.1	n.616-13182A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20554 AN: 152096 Hom.: 1487 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.0935

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.0969

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.135 AC: 20601 AN: 152214 Hom.: 1497 Cov.: 32 AF XY: 0.140 AC XY: 10424 AN XY: 74428

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.0934

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.0973

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.124

Alfa AF: 0.135 Hom.: 175

Bravo AF: 0.122

Asia WGS AF: 0.183 AC: 635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.44
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1090502; hg19: chr3-70394223;