rs2370025

Variant names:

• chr1-192922893-G-A
• rs2370025
• ENST00000644058.2:n.201+2719C>T

Variant summary

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

The ENST00000644058.2(ENSG00000285280):​n.201+2719C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 151,986 control chromosomes in the GnomAD database, including 14,611 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 0.44 (14611 hom., cov: 33)
• Consequence: ENSG00000285280 ENST00000644058.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.480
• Publications: 2 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=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.555 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.201+2719C>T		intron_variant	Intron 1 of 5
ENSG00000285280	ENST00000644134.1	n.104+2719C>T		intron_variant	Intron 1 of 6
ENSG00000285280	ENST00000644436.1	n.104+2719C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66212 AN: 151870 Hom.: 14588 Cov.: 33

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.528

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.436 AC: 66276 AN: 151986 Hom.: 14611 Cov.: 33 AF XY: 0.440 AC XY: 32683 AN XY: 74276

African (AFR) AF: 0.501 AC: 20762 AN: 41444

American (AMR) AF: 0.409 AC: 6250 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1390 AN: 3466

East Asian (EAS) AF: 0.491 AC: 2539 AN: 5166

South Asian (SAS) AF: 0.573 AC: 2760 AN: 4814

European-Finnish (FIN) AF: 0.453 AC: 4781 AN: 10560

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26279 AN: 67944

Other (OTH) AF: 0.425 AC: 898 AN: 2114

Alfa AF: 0.400 Hom.: 1637

Bravo AF: 0.432

Asia WGS AF: 0.560 AC: 1939 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.12
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs2370025; hg19: chr1-192892023;