ENST00000449169.1:n.175+6195T>C

Variant names:

• chr1-110332802-A-G
• rs11102091
• ENST00000449169.1:n.175+6195T>C

Variant summary

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

The ENST00000449169.1(RBM15-AS1):​n.175+6195T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 151,860 control chromosomes in the GnomAD database, including 26,139 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 0.58 (26139 hom., cov: 30)
• Consequence: RBM15-AS1 ENST00000449169.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.915
• Publications: 4 publications found

Genes affected

RBM15-AS1 (HGNC:53636): (RBM15 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RBM15-AS1	NR_036595.1	n.175+6195T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RBM15-AS1	ENST00000449169.1	n.175+6195T>C		intron_variant	Intron 1 of 3	1
RBM15-AS1	ENST00000686992.2	n.220+6195T>C		intron_variant	Intron 1 of 2
RBM15-AS1	ENST00000748880.1	n.179+6195T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88768 AN: 151742 Hom.: 26126 Cov.: 30

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.585 AC: 88834 AN: 151860 Hom.: 26139 Cov.: 30 AF XY: 0.581 AC XY: 43111 AN XY: 74194

African (AFR) AF: 0.653 AC: 27028 AN: 41366

American (AMR) AF: 0.613 AC: 9344 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1677 AN: 3466

East Asian (EAS) AF: 0.496 AC: 2564 AN: 5168

South Asian (SAS) AF: 0.562 AC: 2706 AN: 4814

European-Finnish (FIN) AF: 0.513 AC: 5415 AN: 10556

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.564 AC: 38334 AN: 67930

Other (OTH) AF: 0.557 AC: 1170 AN: 2102

Alfa AF: 0.581 Hom.: 6535

Bravo AF: 0.593

Asia WGS AF: 0.508 AC: 1766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.58
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs11102091; hg19: chr1-110875424;