rs10511000

Variant names:

• chr3-70518202-G-A
• rs10511000
• ENST00000641053.1:n.*138G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-70518202-G-A
• chr3-70518202-G-T

Variant summary

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

The ENST00000641053.1(SAMMSON):​n.*138G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 151,726 control chromosomes in the GnomAD database, including 5,350 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 0.23 (5350 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: SAMMSON ENST00000641053.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.210
• Publications: 6 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.333 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.*138G>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34610 AN: 151608 Hom.: 5352 Cov.: 32

Gnomad AFR AF: 0.0558

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.000586

Gnomad SAS AF: 0.0986

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.228 AC: 34605 AN: 151726 Hom.: 5350 Cov.: 32 AF XY: 0.226 AC XY: 16774 AN XY: 74108

African (AFR) AF: 0.0556 AC: 2306 AN: 41456

American (AMR) AF: 0.203 AC: 3084 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1053 AN: 3468

East Asian (EAS) AF: 0.000587 AC: 3 AN: 5110

South Asian (SAS) AF: 0.0991 AC: 477 AN: 4812

European-Finnish (FIN) AF: 0.368 AC: 3876 AN: 10528

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.337 AC: 22863 AN: 67816

Other (OTH) AF: 0.250 AC: 527 AN: 2108

Alfa AF: 0.276 Hom.: 3627

Bravo AF: 0.209

Asia WGS AF: 0.0510 AC: 177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.2
DANN	Benign	0.52
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs10511000; hg19: chr3-70567353;