chr3-8098092-G-A

Variant names:

• chr3-8098092-G-A
• rs527498
• ENST00000428171.1:n.437+881G>A

Variant summary

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

The ENST00000428171.1(ENSG00000228351):​n.437+881G>A variant causes a intron 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: ENSG00000228351 ENST00000428171.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173
• Publications: 1 publications found

Genes affected

ENSG00000228351 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000428171.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228351	ENST00000428171.1	TSL:4	n.437+881G>A		intron	N/A
	LMCD1-AS1	ENST00000446281.5	TSL:5	n.515-105790C>T		intron	N/A
	ENSG00000228351	ENST00000649560.2		n.656+881G>A		intron	N/A

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

African (AFR) AF: 0.335 AC: 13887 AN: 41400

American (AMR) AF: 0.403 AC: 6145 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1138 AN: 3470

East Asian (EAS) AF: 0.450 AC: 2315 AN: 5146

South Asian (SAS) AF: 0.448 AC: 2158 AN: 4816

European-Finnish (FIN) AF: 0.414 AC: 4364 AN: 10542

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.362 AC: 24572 AN: 67942

Other (OTH) AF: 0.335 AC: 707 AN: 2112

Alfa AF: 0.286 Hom.: 1221

Bravo AF: 0.364

Asia WGS AF: 0.442 AC: 1538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.44
DANN	Benign	0.72
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs527498; hg19: chr3-8139779;