3-8100035-T-C

Variant names:

• chr3-8100035-T-C
• rs9852802
• ENST00000428171.1:n.437+2824T>C

Variant summary

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

The ENST00000428171.1(ENSG00000228351):​n.437+2824T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 151,960 control chromosomes in the GnomAD database, including 25,228 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 0.57 (25228 hom., cov: 32)
• Consequence: ENSG00000228351 ENST00000428171.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299

Genes affected

ENSG00000228351 (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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228351	ENST00000428171.1	n.437+2824T>C		intron_variant	Intron 4 of 5	4
LMCD1-AS1	ENST00000446281.5	n.515-107733A>G		intron_variant	Intron 3 of 5	5
ENSG00000228351	ENST00000649560.2	n.656+2824T>C		intron_variant	Intron 5 of 9

Frequencies

GnomAD3 genomes AF: 0.573 AC: 87018 AN: 151842 Hom.: 25208 Cov.: 32

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.701

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.573 AC: 87077 AN: 151960 Hom.: 25228 Cov.: 32 AF XY: 0.570 AC XY: 42299 AN XY: 74258

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.564

Gnomad4 ASJ AF: 0.664

Gnomad4 EAS AF: 0.549

Gnomad4 SAS AF: 0.520

Gnomad4 FIN AF: 0.587

Gnomad4 NFE AF: 0.621

Gnomad4 OTH AF: 0.616

Alfa AF: 0.605 Hom.: 12099

Bravo AF: 0.567

Asia WGS AF: 0.528 AC: 1834 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.8
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9852802; hg19: chr3-8141722;