rs7311958

Variant names:

• chr12-57219642-C-T
• rs7311958
• NM_007224.4:c.57+2616C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_007224.4(NXPH4):​c.57+2616C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 152,046 control chromosomes in the GnomAD database, including 23,794 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 0.54 (23794 hom., cov: 32)
• Consequence: NXPH4 NM_007224.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.53
• Publications: 4 publications found

Genes affected

NXPH4 (HGNC:8078): (neurexophilin 4) Predicted to enable signaling receptor binding activity. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007224.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NXPH4	NM_007224.4	MANE Select	c.57+2616C>T		intron	N/A	NP_009155.1	O95158

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NXPH4	ENST00000349394.6	TSL:1 MANE Select	c.57+2616C>T		intron	N/A	ENSP00000333593.6	O95158
	NXPH4	ENST00000556415.1	TSL:2	n.58-1665C>T		intron	N/A	ENSP00000452288.1	G3V5C5
	NXPH4	ENST00000555154.1	TSL:3	n.-227C>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81347 AN: 151928 Hom.: 23790 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.535 AC: 81362 AN: 152046 Hom.: 23794 Cov.: 32 AF XY: 0.537 AC XY: 39879 AN XY: 74302

African (AFR) AF: 0.289 AC: 11987 AN: 41490

American (AMR) AF: 0.538 AC: 8228 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2223 AN: 3472

East Asian (EAS) AF: 0.461 AC: 2362 AN: 5124

South Asian (SAS) AF: 0.747 AC: 3603 AN: 4826

European-Finnish (FIN) AF: 0.595 AC: 6281 AN: 10564

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.659 AC: 44757 AN: 67962

Other (OTH) AF: 0.562 AC: 1188 AN: 2114

Alfa AF: 0.591 Hom.: 4907

Bravo AF: 0.509

Asia WGS AF: 0.538 AC: 1872 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	20
DANN	Benign	0.82
PhyloP100		1.5
Mutation Taster		=99/1	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: rs7311958; hg19: chr12-57613425;