rs72840936

chr2-119266116-G-C

Variant summary

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

The XR_001739666.3(LOC105373581):n.3722C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0314 in 152,228 control chromosomes in the GnomAD database, including 92 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 0.031 (92 hom., cov: 32)
• Consequence: LOC105373581 XR_001739666.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.950

Genes affected

LOC105373581 (HGNC:):

STEAP3-AS1 (HGNC:41053): (STEAP3 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0863 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373581	XR_001739666.3	n.3722C>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STEAP3-AS1	ENST00000654197.1	n.111+3319C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0314 AC: 4777 AN: 152110 Hom.: 92 Cov.: 32

Gnomad AFR AF: 0.0146

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0220

Gnomad ASJ AF: 0.0844

Gnomad EAS AF: 0.00771

Gnomad SAS AF: 0.0934

Gnomad FIN AF: 0.0118

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0413

Gnomad OTH AF: 0.0383

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

GnomAD4 genome AF: 0.0314 AC: 4779 AN: 152228 Hom.: 92 Cov.: 32 AF XY: 0.0308 AC XY: 2295 AN XY: 74438

Gnomad4 AFR AF: 0.0145

Gnomad4 AMR AF: 0.0220

Gnomad4 ASJ AF: 0.0844

Gnomad4 EAS AF: 0.00812

Gnomad4 SAS AF: 0.0935

Gnomad4 FIN AF: 0.0118

Gnomad4 NFE AF: 0.0413

Gnomad4 OTH AF: 0.0388

Alfa AF: 0.0340 Hom.: 14

Bravo AF: 0.0306

Asia WGS AF: 0.0630 AC: 218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	7.4
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs72840936; hg19: chr2-120023692; COSMIC: COSV61531221;