rs6671323

Variant names:

• chr1-110302918-A-T
• rs6671323
• ENST00000449169.1:n.294-10411T>A

Variant summary

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

The ENST00000449169.1(RBM15-AS1):​n.294-10411T>A variant causes a intron 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 ENST00000449169.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.782
• Publications: 1 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=-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 rank	MANE	Protein	UniProt
RBM15-AS1	NR_036595.1	n.294-10411T>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RBM15-AS1	ENST00000449169.1	n.294-10411T>A		intron_variant	Intron 2 of 3	1
RBM15-AS1	ENST00000686992.2	n.339-10411T>A		intron_variant	Intron 2 of 2
RBM15-AS1	ENST00000748880.1	n.180-10411T>A		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.174 AC: 7236 AN: 41520

American (AMR) AF: 0.210 AC: 3209 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 666 AN: 3466

East Asian (EAS) AF: 0.0597 AC: 309 AN: 5180

South Asian (SAS) AF: 0.246 AC: 1185 AN: 4826

European-Finnish (FIN) AF: 0.335 AC: 3543 AN: 10586

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.334 AC: 22710 AN: 67974

Other (OTH) AF: 0.233 AC: 492 AN: 2114

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
PhyloP100		-0.78
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs6671323; hg19: chr1-110845540;