rs13317787

Variant names:

• chr3-8100265-C-A
• rs13317787
• ENST00000428171.1:n.437+3054C>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+3054C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0646 in 152,276 control chromosomes in the GnomAD database, including 679 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 0.065 (679 hom., cov: 33)
• Consequence: ENSG00000228351 ENST00000428171.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.346
• Publications: 3 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.171 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+3054C>A		intron_variant	Intron 4 of 5	4
LMCD1-AS1	ENST00000446281.5	n.515-107963G>T		intron_variant	Intron 3 of 5	5
ENSG00000228351	ENST00000649560.2	n.656+3054C>A		intron_variant	Intron 5 of 9

Frequencies

GnomAD3 genomes AF: 0.0644 AC: 9806 AN: 152158 Hom.: 675 Cov.: 33

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0353

Gnomad ASJ AF: 0.00806

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0362

Gnomad FIN AF: 0.00819

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0243

Gnomad OTH AF: 0.0517

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

GnomAD4 genome AF: 0.0646 AC: 9832 AN: 152276 Hom.: 679 Cov.: 33 AF XY: 0.0634 AC XY: 4719 AN XY: 74466

African (AFR) AF: 0.174 AC: 7231 AN: 41536

American (AMR) AF: 0.0352 AC: 539 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00806 AC: 28 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.0360 AC: 174 AN: 4828

European-Finnish (FIN) AF: 0.00819 AC: 87 AN: 10622

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0243 AC: 1654 AN: 68024

Other (OTH) AF: 0.0511 AC: 108 AN: 2112

Alfa AF: 0.0379 Hom.: 812

Bravo AF: 0.0720

Asia WGS AF: 0.0310 AC: 110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.66
DANN	Benign	0.26
PhyloP100		-0.35
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs13317787; hg19: chr3-8141952;