rs1363793

Variant names:

• chr5-57578607-G-A
• rs1363793
• ENST00000513392.2:n.122-229G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-57578607-G-A
• chr5-57578607-G-C

Variant summary

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

The ENST00000513392.2(LNCBRM):​n.122-229G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.807 in 152,150 control chromosomes in the GnomAD database, including 49,625 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 0.81 (49625 hom., cov: 31)
• Consequence: LNCBRM ENST00000513392.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 3 publications found

Genes affected

LNCBRM (HGNC:52752): (lncRNA SMARCA2 (BRM) associated)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LNCBRM	NR_120607.1	n.203-229G>A		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LNCBRM	ENST00000513392.2	n.122-229G>A		intron_variant	Intron 2 of 5	5
LNCBRM	ENST00000660175.1	n.293-229G>A		intron_variant	Intron 2 of 4
LNCBRM	ENST00000663255.1	n.163-229G>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.807 AC: 122661 AN: 152032 Hom.: 49593 Cov.: 31

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.929

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.810

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.816

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

GnomAD4 genome AF: 0.807 AC: 122751 AN: 152150 Hom.: 49625 Cov.: 31 AF XY: 0.803 AC XY: 59743 AN XY: 74406

African (AFR) AF: 0.818 AC: 33938 AN: 41512

American (AMR) AF: 0.784 AC: 11991 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.799 AC: 2770 AN: 3468

East Asian (EAS) AF: 0.598 AC: 3077 AN: 5146

South Asian (SAS) AF: 0.751 AC: 3624 AN: 4828

European-Finnish (FIN) AF: 0.810 AC: 8578 AN: 10592

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.823 AC: 55968 AN: 67998

Other (OTH) AF: 0.816 AC: 1724 AN: 2112

Alfa AF: 0.813 Hom.: 26987

Bravo AF: 0.805

Asia WGS AF: 0.676 AC: 2350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.019
DANN	Benign	0.55
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1363793; hg19: chr5-56874434;