rs1024889

chr3-70414179-A-G

Variant summary

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

The ENST00000641053.1(SAMMSON):n.234-48381A>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 0.251 in 151,976 control chromosomes in the GnomAD database, including 5,344 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 0.25 (5344 hom., cov: 32)
• Consequence: SAMMSON ENST00000641053.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.43

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=-0.53).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SAMMSON	ENST00000641053.1	n.234-48381A>G		intron_variant, non_coding_transcript_variant
SAMMSON	ENST00000641222.1	n.687-10598A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38163 AN: 151858 Hom.: 5342 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.0411

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.251 AC: 38180 AN: 151976 Hom.: 5344 Cov.: 32 AF XY: 0.245 AC XY: 18194 AN XY: 74290

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.0408

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.261

Alfa AF: 0.304 Hom.: 11354

Bravo AF: 0.243

Asia WGS AF: 0.111 AC: 387 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
Cadd	Benign	16
Dann	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1024889; hg19: chr3-70463330;