rs1616547

Positions:

• chr13-79411901-A-C
• chr13-79411901-A-T

Variant summary

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

The NR_038991.1(RBM26-AS1):​n.170-781A>C 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 0.455 in 152,054 control chromosomes in the GnomAD database, including 16,229 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 0.46 (16229 hom., cov: 32)
• Consequence: RBM26-AS1 NR_038991.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180

Genes affected

RBM26-AS1 (HGNC:39805): (RBM26 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RBM26-AS1	NR_038991.1	n.170-781A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RBM26-AS1	ENST00000656024.1	n.178-781A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69234 AN: 151936 Hom.: 16224 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.455 AC: 69254 AN: 152054 Hom.: 16229 Cov.: 32 AF XY: 0.451 AC XY: 33533 AN XY: 74340

Gnomad4 AFR AF: 0.390

Gnomad4 AMR AF: 0.390

Gnomad4 ASJ AF: 0.596

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.530

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.462

Alfa AF: 0.337 Hom.: 863

Bravo AF: 0.447

Asia WGS AF: 0.407 AC: 1419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	11
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1616547; hg19: chr13-79986036;