17-46922868-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The XM_024450773.2(LRRC37A2):​c.4810-126188C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00591 in 453,476 control chromosomes in the GnomAD database, including 56 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.014 ( 53 hom., cov: 32)
Exomes 𝑓: 0.0016 ( 3 hom. )

Consequence

LRRC37A2
XM_024450773.2 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.888
Variant links:
Genes affected
LRRC37A2 (HGNC:32404): (leucine rich repeat containing 37 member A2) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
GOSR2-DT (HGNC:55346): (GOSR2 divergent transcript)
GOSR2 (HGNC:4431): (golgi SNAP receptor complex member 2) This gene encodes a trafficking membrane protein which transports proteins among the medial- and trans-Golgi compartments. Due to its chromosomal location and trafficking function, this gene may be involved in familial essential hypertension. [provided by RefSeq, Mar 2016]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP6
Variant 17-46922868-C-T is Benign according to our data. Variant chr17-46922868-C-T is described in ClinVar as [Benign]. Clinvar id is 1241591.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0144 (2187/152328) while in subpopulation AFR AF= 0.0503 (2090/41572). AF 95% confidence interval is 0.0485. There are 53 homozygotes in gnomad4. There are 1020 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 53 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LRRC37A2XM_024450773.2 linkc.4810-126188C>T intron_variant Intron 10 of 10 XP_024306541.1
GOSR2-DTNR_186460.1 linkn.4G>A non_coding_transcript_exon_variant Exon 1 of 3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GOSR2-DTENST00000572349.1 linkn.167G>A non_coding_transcript_exon_variant Exon 1 of 3 3
GOSR2ENST00000640608.1 linkc.-325C>T upstream_gene_variant 2 ENSP00000491979.1 A0A1W2PR02
GOSR2ENST00000638634.1 linkc.-325C>T upstream_gene_variant 5 ENSP00000491946.1 A0A1W2PQ77

Frequencies

GnomAD3 genomes
AF:
0.0142
AC:
2168
AN:
152210
Hom.:
52
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0500
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00412
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.000191
Gnomad OTH
AF:
0.00909
GnomAD4 exome
AF:
0.00163
AC:
492
AN:
301148
Hom.:
3
Cov.:
0
AF XY:
0.00125
AC XY:
198
AN XY:
157994
show subpopulations
Gnomad4 AFR exome
AF:
0.0429
Gnomad4 AMR exome
AF:
0.00313
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000120
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000715
Gnomad4 OTH exome
AF:
0.00319
GnomAD4 genome
AF:
0.0144
AC:
2187
AN:
152328
Hom.:
53
Cov.:
32
AF XY:
0.0137
AC XY:
1020
AN XY:
74484
show subpopulations
Gnomad4 AFR
AF:
0.0503
Gnomad4 AMR
AF:
0.00412
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000191
Gnomad4 OTH
AF:
0.00900
Alfa
AF:
0.0112
Hom.:
2
Bravo
AF:
0.0164
Asia WGS
AF:
0.00318
AC:
11
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Jun 22, 2018
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.75
CADD
Benign
12
DANN
Benign
0.84

Splicing

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: rs55904085; hg19: chr17-45000234; API