9-12788785-G-T

Variant names:

• chr9-12788785-G-T
• rs7867305
• NM_203403.2:c.312+12758G>T

Variant summary

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

The NM_203403.2(LURAP1L):​c.312+12758G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 151,742 control chromosomes in the GnomAD database, including 42,315 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 0.74 (42315 hom., cov: 31)
• Consequence: LURAP1L NM_203403.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123
• Publications: 2 publications found

Genes affected

LURAP1L (HGNC:31452): (leucine rich adaptor protein 1 like) Predicted to be involved in positive regulation of I-kappaB kinase/NF-kappaB signaling. [provided by Alliance of Genome Resources, Apr 2022]

LURAP1L-AS1 (HGNC:49761): (LURAP1L antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LURAP1L	NM_203403.2	c.312+12758G>T		intron_variant	Intron 1 of 1	ENST00000319264.4	NP_981948.1
LURAP1L-AS1	NR_125775.1	n.243+1835C>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LURAP1L	ENST00000319264.4	c.312+12758G>T		intron_variant	Intron 1 of 1	1	NM_203403.2	ENSP00000321026.3
LURAP1L-AS1	ENST00000417638.1	n.199+1835C>A		intron_variant	Intron 2 of 3	3
LURAP1L-AS1	ENST00000803542.1	n.236+1835C>A		intron_variant	Intron 2 of 3
LURAP1L-AS1	ENST00000803546.1	n.235+1835C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.744 AC: 112783 AN: 151624 Hom.: 42269 Cov.: 31

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.790

Gnomad AMR AF: 0.734

Gnomad ASJ AF: 0.742

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.744 AC: 112882 AN: 151742 Hom.: 42315 Cov.: 31 AF XY: 0.740 AC XY: 54911 AN XY: 74156

African (AFR) AF: 0.823 AC: 34064 AN: 41412

American (AMR) AF: 0.734 AC: 11186 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.742 AC: 2573 AN: 3466

East Asian (EAS) AF: 0.644 AC: 3330 AN: 5170

South Asian (SAS) AF: 0.719 AC: 3463 AN: 4816

European-Finnish (FIN) AF: 0.664 AC: 6916 AN: 10414

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.719 AC: 48841 AN: 67914

Other (OTH) AF: 0.746 AC: 1569 AN: 2102

Alfa AF: 0.722 Hom.: 34578

Bravo AF: 0.748

Asia WGS AF: 0.732 AC: 2533 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.64
DANN	Benign	0.42
PhyloP100		-0.12
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7867305; hg19: chr9-12788784;