rs2746071

Variant names:

• chr1-192808434-A-G
• rs2746071
• ENST00000644058.2:n.202-42240T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-192808434-A-G
• chr1-192808434-A-T

Variant summary

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

The ENST00000644058.2(ENSG00000285280):​n.202-42240T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 152,068 control chromosomes in the GnomAD database, including 9,628 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 0.35 (9628 hom., cov: 32)
• Consequence: ENSG00000285280 ENST00000644058.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.523
• Publications: 17 publications found

Genes affected

ENSG00000285280 (HGNC:49018): (RSG2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.481 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
ENSG00000285280	ENST00000644058.2	n.202-42240T>C		intron_variant	Intron 1 of 5
ENSG00000285280	ENST00000644134.1	n.105-42240T>C		intron_variant	Intron 1 of 6
ENSG00000285280	ENST00000645822.1	n.200-15966T>C		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52572 AN: 151950 Hom.: 9626 Cov.: 32

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.346 AC: 52603 AN: 152068 Hom.: 9628 Cov.: 32 AF XY: 0.346 AC XY: 25740 AN XY: 74338

African (AFR) AF: 0.462 AC: 19184 AN: 41480

American (AMR) AF: 0.347 AC: 5306 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1097 AN: 3472

East Asian (EAS) AF: 0.497 AC: 2570 AN: 5172

South Asian (SAS) AF: 0.292 AC: 1406 AN: 4808

European-Finnish (FIN) AF: 0.259 AC: 2745 AN: 10584

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19125 AN: 67950

Other (OTH) AF: 0.326 AC: 687 AN: 2108

Alfa AF: 0.303 Hom.: 9322

Bravo AF: 0.358

Asia WGS AF: 0.425 AC: 1473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.7
DANN	Benign	0.36
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs2746071; hg19: chr1-192777564;