rs17790790

Variant names:

• chr3-70516669-G-A
• rs17790790
• ENST00000641053.1:n.337-216G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000641053.1(SAMMSON):​n.337-216G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 151,572 control chromosomes in the GnomAD database, including 24,141 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 (24141 hom., cov: 31)
• Consequence: SAMMSON ENST00000641053.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SAMMSON	ENST00000641053.1	n.337-216G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.561 AC: 84920 AN: 151454 Hom.: 24113 Cov.: 31

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.554

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.561 AC: 84998 AN: 151572 Hom.: 24141 Cov.: 31 AF XY: 0.563 AC XY: 41652 AN XY: 74024

African (AFR) AF: 0.520 AC: 21496 AN: 41374

American (AMR) AF: 0.656 AC: 9982 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1943 AN: 3464

East Asian (EAS) AF: 0.681 AC: 3454 AN: 5070

South Asian (SAS) AF: 0.700 AC: 3368 AN: 4814

European-Finnish (FIN) AF: 0.501 AC: 5281 AN: 10538

Middle Eastern (MID) AF: 0.627 AC: 183 AN: 292

European-Non Finnish (NFE) AF: 0.554 AC: 37535 AN: 67778

Other (OTH) AF: 0.578 AC: 1221 AN: 2112

Alfa AF: 0.567 Hom.: 41104

Bravo AF: 0.570

Asia WGS AF: 0.675 AC: 2344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.0050
DANN	Benign	0.21
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs17790790; hg19: chr3-70565820;