rs1491609

Positions:

• chr3-70501311-C-A
• chr3-70501311-C-G
• chr3-70501311-C-T

Variant summary

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

The ENST00000641053.1(SAMMSON):​n.337-15574C>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 0.56 in 151,378 control chromosomes in the GnomAD database, including 24,068 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 0.56 (24068 hom., cov: 31)
• Consequence: SAMMSON ENST00000641053.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440

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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.679 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	ENST00000641053.1	n.337-15574C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.560 AC: 84730 AN: 151260 Hom.: 24031 Cov.: 31

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.560 AC: 84824 AN: 151378 Hom.: 24068 Cov.: 31 AF XY: 0.563 AC XY: 41660 AN XY: 73936

Gnomad4 AFR AF: 0.550

Gnomad4 AMR AF: 0.657

Gnomad4 ASJ AF: 0.558

Gnomad4 EAS AF: 0.686

Gnomad4 SAS AF: 0.699

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.536

Gnomad4 OTH AF: 0.580

Alfa AF: 0.477 Hom.: 2187

Bravo AF: 0.572

Asia WGS AF: 0.682 AC: 2365 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1491609; hg19: chr3-70550462;