chr3-70434079-C-T

Variant names:

• chr3-70434079-C-T
• rs1073810
• NR_186031.1:n.4560C>T

Variant summary

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

The NR_186031.1(SAMMSON):​n.4560C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,066 control chromosomes in the GnomAD database, including 1,350 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 0.12 (1350 hom., cov: 32)
• Consequence: SAMMSON NR_186031.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.713

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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SAMMSON	NR_186031.1	n.4560C>T		non_coding_transcript_exon_variant	Exon 7 of 7
SAMMSON	NR_186032.1	n.4704C>T		non_coding_transcript_exon_variant	Exon 9 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SAMMSON	ENST00000641053.1	n.234-28481C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18109 AN: 151948 Hom.: 1336 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0929

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.119 AC: 18140 AN: 152066 Hom.: 1350 Cov.: 32 AF XY: 0.124 AC XY: 9241 AN XY: 74346

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.0929

Gnomad4 OTH AF: 0.126

Alfa AF: 0.107 Hom.: 143

Bravo AF: 0.122

Asia WGS AF: 0.316 AC: 1095 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.1
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1073810; hg19: chr3-70483230;