rs10808265

Variant names:

• chr7-132504930-G-A
• rs10808265
• NM_020911.2:c.1188+2576C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-132504930-G-A
• chr7-132504930-G-T

Variant summary

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

The NM_020911.2(PLXNA4):​c.1188+2576C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 152,172 control chromosomes in the GnomAD database, including 9,977 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 0.33 (9977 hom., cov: 33)
• Consequence: PLXNA4 NM_020911.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.803
• Publications: 11 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLXNA4	NM_020911.2	c.1188+2576C>T		intron_variant	Intron 2 of 31	ENST00000321063.9	NP_065962.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLXNA4	ENST00000321063.9	c.1188+2576C>T		intron_variant	Intron 2 of 31	5	NM_020911.2	ENSP00000323194.4
PLXNA4	ENST00000378539.5	c.1188+2576C>T		intron_variant	Intron 3 of 4	1		ENSP00000367800.5
PLXNA4	ENST00000359827.7	c.1188+2576C>T		intron_variant	Intron 2 of 31	5		ENSP00000352882.3
PLXNA4	ENST00000423507.6	c.1188+2576C>T		intron_variant	Intron 2 of 3	2		ENSP00000392772.2

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50908 AN: 152054 Hom.: 9987 Cov.: 33

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.334 AC: 50894 AN: 152172 Hom.: 9977 Cov.: 33 AF XY: 0.337 AC XY: 25068 AN XY: 74380

African (AFR) AF: 0.127 AC: 5284 AN: 41556

American (AMR) AF: 0.360 AC: 5506 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1192 AN: 3470

East Asian (EAS) AF: 0.486 AC: 2500 AN: 5144

South Asian (SAS) AF: 0.497 AC: 2396 AN: 4824

European-Finnish (FIN) AF: 0.333 AC: 3527 AN: 10582

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.431 AC: 29274 AN: 67992

Other (OTH) AF: 0.345 AC: 729 AN: 2116

Alfa AF: 0.403 Hom.: 42395

Bravo AF: 0.325

Asia WGS AF: 0.451 AC: 1568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	8.6
DANN	Benign	0.85
PhyloP100		0.80
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: rs10808265; hg19: chr7-132189689;