3-141689849-A-G

Variant names:

• chr3-141689849-A-G
• rs6440031
• ENST00000474979.4:n.874-583A>G

Variant summary

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

The ENST00000474979.4(ENSG00000293386):​n.874-583A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.925 in 152,162 control chromosomes in the GnomAD database, including 65,173 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 0.92 (65173 hom., cov: 30)
• Consequence: ENSG00000293386 ENST00000474979.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.622
• Publications: 3 publications found

Genes affected

ENSG00000293386 (HGNC:54091): (long intergenic non-protein coding RNA 2618)

LRRC78P (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRC78P	NR_136190.1	n.663-583A>G		intron_variant	Intron 5 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293386	ENST00000474979.4	n.874-583A>G		intron_variant	Intron 6 of 9	5
LRRC78P	ENST00000637590.2	n.770-583A>G		intron_variant	Intron 5 of 8	6
ENSG00000293386	ENST00000819704.1	n.746-583A>G		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.925 AC: 140630 AN: 152044 Hom.: 65113 Cov.: 30

Gnomad AFR AF: 0.966

Gnomad AMI AF: 0.985

Gnomad AMR AF: 0.938

Gnomad ASJ AF: 0.905

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.892

Gnomad FIN AF: 0.910

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.900

Gnomad OTH AF: 0.922

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

GnomAD4 genome AF: 0.925 AC: 140749 AN: 152162 Hom.: 65173 Cov.: 30 AF XY: 0.927 AC XY: 68941 AN XY: 74368

African (AFR) AF: 0.966 AC: 40075 AN: 41504

American (AMR) AF: 0.938 AC: 14335 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.905 AC: 3141 AN: 3472

East Asian (EAS) AF: 0.962 AC: 4981 AN: 5176

South Asian (SAS) AF: 0.892 AC: 4296 AN: 4818

European-Finnish (FIN) AF: 0.910 AC: 9638 AN: 10596

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.900 AC: 61166 AN: 67998

Other (OTH) AF: 0.923 AC: 1951 AN: 2114

Alfa AF: 0.907 Hom.: 109395

Bravo AF: 0.928

Asia WGS AF: 0.915 AC: 3183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.46
DANN	Benign	0.32
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs6440031; hg19: chr3-141408691;