rs1019374

Positions:

• chr3-70420625-T-A

Variant summary

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

The ENST00000641053.1(SAMMSON):​n.234-41935T>A 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 0.22 in 152,146 control chromosomes in the GnomAD database, including 4,705 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 0.22 (4705 hom., cov: 33)
• Consequence: SAMMSON ENST00000641053.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119

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=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SAMMSON	ENST00000641053.1	n.234-41935T>A		intron_variant, non_coding_transcript_variant
SAMMSON	ENST00000641222.1	n.687-4152T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33440 AN: 152028 Hom.: 4706 Cov.: 33

Gnomad AFR AF: 0.0699

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.0406

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.220 AC: 33428 AN: 152146 Hom.: 4705 Cov.: 33 AF XY: 0.214 AC XY: 15917 AN XY: 74362

Gnomad4 AFR AF: 0.0697

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.0403

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.240

Alfa AF: 0.271 Hom.: 775

Bravo AF: 0.208

Asia WGS AF: 0.102 AC: 354 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.5
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1019374; hg19: chr3-70469776;