rs6671323

Positions:

• chr1-110302918-A-T

Variant summary

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

The NR_036595.1(RBM15-AS1):​n.294-10411T>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 0.261 in 152,154 control chromosomes in the GnomAD database, including 5,686 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 0.26 (5686 hom., cov: 32)
• Consequence: RBM15-AS1 NR_036595.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.782

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RBM15-AS1	NR_036595.1	n.294-10411T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RBM15-AS1	ENST00000449169.1	n.294-10411T>A		intron_variant, non_coding_transcript_variant		1
RBM15-AS1	ENST00000686992.1	n.276-10411T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39672 AN: 152036 Hom.: 5686 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.0597

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.261 AC: 39679 AN: 152154 Hom.: 5686 Cov.: 32 AF XY: 0.258 AC XY: 19205 AN XY: 74370

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.0597

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.335

Gnomad4 NFE AF: 0.334

Gnomad4 OTH AF: 0.233

Alfa AF: 0.308 Hom.: 938

Bravo AF: 0.243

Asia WGS AF: 0.152 AC: 529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6671323; hg19: chr1-110845540;