rs6973565

Variant summary

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

The NM_020911.2(PLXNA4):​c.1504-16719A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,258 control chromosomes in the GnomAD database, including 2,597 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 0.17 ( 2597 hom., cov: 33)

Consequence

PLXNA4
NM_020911.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.855
Variant links:
Genes affected
PLXNA4 (HGNC:9102): (plexin A4) Predicted to enable semaphorin receptor activity. Predicted to be involved in several processes, including axon guidance; positive regulation of axonogenesis; and regulation of GTPase activity. Predicted to act upstream of or within several processes, including nervous system development; regulation of axon extension involved in axon guidance; and regulation of negative chemotaxis. Predicted to be located in plasma membrane. Predicted to be part of semaphorin receptor complex. Predicted to be integral component of plasma membrane. [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=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PLXNA4NM_020911.2 linkuse as main transcriptc.1504-16719A>T intron_variant ENST00000321063.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PLXNA4ENST00000321063.9 linkuse as main transcriptc.1504-16719A>T intron_variant 5 NM_020911.2 P1Q9HCM2-1
PLXNA4ENST00000359827.7 linkuse as main transcriptc.1504-16719A>T intron_variant 5 P1Q9HCM2-1

Frequencies

GnomAD3 genomes
AF:
0.175
AC:
26567
AN:
152138
Hom.:
2589
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.251
Gnomad AMI
AF:
0.0811
Gnomad AMR
AF:
0.139
Gnomad ASJ
AF:
0.187
Gnomad EAS
AF:
0.00963
Gnomad SAS
AF:
0.121
Gnomad FIN
AF:
0.161
Gnomad MID
AF:
0.133
Gnomad NFE
AF:
0.156
Gnomad OTH
AF:
0.175
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.175
AC:
26617
AN:
152258
Hom.:
2597
Cov.:
33
AF XY:
0.174
AC XY:
12936
AN XY:
74456
show subpopulations
Gnomad4 AFR
AF:
0.251
Gnomad4 AMR
AF:
0.139
Gnomad4 ASJ
AF:
0.187
Gnomad4 EAS
AF:
0.00965
Gnomad4 SAS
AF:
0.123
Gnomad4 FIN
AF:
0.161
Gnomad4 NFE
AF:
0.156
Gnomad4 OTH
AF:
0.174
Alfa
AF:
0.165
Hom.:
281
Bravo
AF:
0.173
Asia WGS
AF:
0.0730
AC:
257
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.12
DANN
Benign
0.49

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: rs6973565; hg19: chr7-131942644; API