1-4717567-A-T

Variant names:

• chr1-4717567-A-T
• rs16839502
• NM_018836.4:c.829+4868A>T

Variant summary

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

The NM_018836.4(AJAP1):​c.829+4868A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,212 control chromosomes in the GnomAD database, including 1,714 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 0.11 (1714 hom., cov: 32)
• Consequence: AJAP1 NM_018836.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310
• Publications: 2 publications found

Genes affected

AJAP1 (HGNC:30801): (adherens junctions associated protein 1) Enables beta-catenin binding activity. Involved in negative regulation of cell-matrix adhesion; negative regulation of wound healing; and regulation of polarized epithelial cell differentiation. Located in several cellular components, including adherens junction; basolateral plasma membrane; and cell-cell contact zone. Is spanning 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=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018836.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AJAP1	NM_018836.4	MANE Select	c.829+4868A>T		intron	N/A	NP_061324.1
	AJAP1	NM_001042478.2		c.829+4868A>T		intron	N/A	NP_001035943.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AJAP1	ENST00000378191.5	TSL:1 MANE Select	c.829+4868A>T		intron	N/A	ENSP00000367433.3
	AJAP1	ENST00000378190.7	TSL:5	c.829+4868A>T		intron	N/A	ENSP00000367432.3
	AJAP1	ENST00000880749.1		c.829+4868A>T		intron	N/A	ENSP00000550808.1

Frequencies

GnomAD3 genomes AF: 0.105 AC: 16018 AN: 152094 Hom.: 1710 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.0531

Gnomad ASJ AF: 0.0462

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.0739

Gnomad FIN AF: 0.0683

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.0332

Gnomad OTH AF: 0.0827

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

GnomAD4 genome AF: 0.105 AC: 16043 AN: 152212 Hom.: 1714 Cov.: 32 AF XY: 0.105 AC XY: 7811 AN XY: 74416

African (AFR) AF: 0.274 AC: 11371 AN: 41512

American (AMR) AF: 0.0530 AC: 810 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0462 AC: 160 AN: 3460

East Asian (EAS) AF: 0.0137 AC: 71 AN: 5170

South Asian (SAS) AF: 0.0742 AC: 358 AN: 4828

European-Finnish (FIN) AF: 0.0683 AC: 725 AN: 10612

Middle Eastern (MID) AF: 0.110 AC: 32 AN: 292

European-Non Finnish (NFE) AF: 0.0332 AC: 2257 AN: 68026

Other (OTH) AF: 0.0814 AC: 172 AN: 2114

Alfa AF: 0.0128 Hom.: 9

Bravo AF: 0.111

Asia WGS AF: 0.0560 AC: 198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	0.84
DANN	Benign	0.64
PhyloP100		0.031
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: rs16839502; hg19: chr1-4777627; COSMIC: COSV65449915;