rs527498

Positions:

• chr3-8098092-G-A
• chr3-8098092-G-C
• chr3-8098092-G-T

Variant summary

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

The ENST00000649560.2(ENSG00000228351):​n.656+881G>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 0.367 in 151,890 control chromosomes in the GnomAD database, including 10,256 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 0.37 (10256 hom., cov: 33)
• Consequence: ENST00000649560.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173

Genes affected

(HGNC:):

LMCD1-AS1 (HGNC:44477): (LMCD1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000649560.2	n.656+881G>A		intron_variant, non_coding_transcript_variant
LMCD1-AS1	ENST00000654635.1	n.746+96824C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55642 AN: 151772 Hom.: 10248 Cov.: 33

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.367 AC: 55676 AN: 151890 Hom.: 10256 Cov.: 33 AF XY: 0.372 AC XY: 27584 AN XY: 74240

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.328

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.335

Alfa AF: 0.284 Hom.: 1168

Bravo AF: 0.364

Asia WGS AF: 0.442 AC: 1538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.44
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs527498; hg19: chr3-8139779;