1-69938857-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001370785.2(LRRC7):​c.711+7287A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 150,936 control chromosomes in the GnomAD database, including 23,302 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 0.55 ( 23302 hom., cov: 28)

Consequence

LRRC7
NM_001370785.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.39
Variant links:
Genes affected
LRRC7 (HGNC:18531): (leucine rich repeat containing 7) Predicted to be involved in several processes, including establishment or maintenance of epithelial cell apical/basal polarity; positive regulation of neuron projection development; and receptor clustering. Located in several cellular components, including centrosome; cytosol; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LRRC7NM_001370785.2 linkuse as main transcriptc.711+7287A>T intron_variant ENST00000651989.2 NP_001357714.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LRRC7ENST00000651989.2 linkuse as main transcriptc.711+7287A>T intron_variant NM_001370785.2 ENSP00000498937.2 A0A494C1A4
LRRC7ENST00000415775.2 linkuse as main transcriptc.-809+7287A>T intron_variant 1 ENSP00000394867.2 F8WE45
LRRC7ENST00000310961.9 linkuse as main transcriptc.612+7287A>T intron_variant 5 ENSP00000309245.4 A0A075B6E9
LRRC7ENST00000651217.1 linkuse as main transcriptn.627+7287A>T intron_variant

Frequencies

GnomAD3 genomes
AF:
0.555
AC:
83651
AN:
150824
Hom.:
23266
Cov.:
28
show subpopulations
Gnomad AFR
AF:
0.560
Gnomad AMI
AF:
0.764
Gnomad AMR
AF:
0.558
Gnomad ASJ
AF:
0.581
Gnomad EAS
AF:
0.703
Gnomad SAS
AF:
0.481
Gnomad FIN
AF:
0.535
Gnomad MID
AF:
0.509
Gnomad NFE
AF:
0.543
Gnomad OTH
AF:
0.568
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.555
AC:
83726
AN:
150936
Hom.:
23302
Cov.:
28
AF XY:
0.552
AC XY:
40640
AN XY:
73682
show subpopulations
Gnomad4 AFR
AF:
0.560
Gnomad4 AMR
AF:
0.557
Gnomad4 ASJ
AF:
0.581
Gnomad4 EAS
AF:
0.703
Gnomad4 SAS
AF:
0.480
Gnomad4 FIN
AF:
0.535
Gnomad4 NFE
AF:
0.543
Gnomad4 OTH
AF:
0.573
Alfa
AF:
0.530
Hom.:
2578
Bravo
AF:
0.561

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
5.8
DANN
Benign
0.37

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1023008; hg19: chr1-70404540; API