rs10510993

Variant names:

• chr3-70011930-A-G
• rs10510993
• ENST00000483525.3:n.137-427A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000483525.3(SAMMSON):​n.137-427A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0186 in 152,194 control chromosomes in the GnomAD database, including 52 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 0.019 (52 hom., cov: 31)
• Consequence: SAMMSON ENST00000483525.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590
• Publications: 1 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=-0.88).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0186 (2826/152194) while in subpopulation AFR AF = 0.036 (1493/41504). AF 95% confidence interval is 0.0345. There are 52 homozygotes in GnomAd4. There are 1404 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 52 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SAMMSON	NR_110000.2	n.136-427A>G		intron_variant	Intron 1 of 3
SAMMSON	NR_186009.1	n.34-427A>G		intron_variant	Intron 1 of 3
SAMMSON	NR_186010.1	n.136-427A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SAMMSON	ENST00000483525.3	n.137-427A>G		intron_variant	Intron 1 of 3	1
SAMMSON	ENST00000488861.7	n.56-427A>G		intron_variant	Intron 1 of 3	3
SAMMSON	ENST00000641005.1	n.243-427A>G		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.0185 AC: 2815 AN: 152078 Hom.: 50 Cov.: 31

Gnomad AFR AF: 0.0358

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0135

Gnomad ASJ AF: 0.0216

Gnomad EAS AF: 0.0131

Gnomad SAS AF: 0.0346

Gnomad FIN AF: 0.00575

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0102

Gnomad OTH AF: 0.0225

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

GnomAD4 genome AF: 0.0186 AC: 2826 AN: 152194 Hom.: 52 Cov.: 31 AF XY: 0.0189 AC XY: 1404 AN XY: 74398

African (AFR) AF: 0.0360 AC: 1493 AN: 41504

American (AMR) AF: 0.0135 AC: 206 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0216 AC: 75 AN: 3470

East Asian (EAS) AF: 0.0132 AC: 68 AN: 5166

South Asian (SAS) AF: 0.0349 AC: 168 AN: 4818

European-Finnish (FIN) AF: 0.00575 AC: 61 AN: 10608

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0102 AC: 693 AN: 68018

Other (OTH) AF: 0.0223 AC: 47 AN: 2110

Alfa AF: 0.0139 Hom.: 6

Bravo AF: 0.0193

Asia WGS AF: 0.0300 AC: 105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.38
PhyloP100		0.059
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10510993; hg19: chr3-70061081;