5-57578607-G-A

Position:

• chr5-57578607-G-A

Variant summary

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

The NR_120607.1(LNCBRM):​n.203-229G>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 0.807 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 NR_120607.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LNCBRM	NR_120607.1	n.203-229G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LNCBRM	ENST00000664455.1	n.166-229G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.818

Gnomad4 AMR AF: 0.784

Gnomad4 ASJ AF: 0.799

Gnomad4 EAS AF: 0.598

Gnomad4 SAS AF: 0.751

Gnomad4 FIN AF: 0.810

Gnomad4 NFE AF: 0.823

Gnomad4 OTH AF: 0.816

Alfa AF: 0.811 Hom.: 24072

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1363793; hg19: chr5-56874434;