rs1483198

Variant names:

• chr1-4657331-A-G
• rs1483198
• NM_018836.4:c.29+1877A>G

Variant summary

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

The NM_018836.4(AJAP1):​c.29+1877A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 151,242 control chromosomes in the GnomAD database, including 2,628 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 (2628 hom., cov: 31)
• Consequence: AJAP1 NM_018836.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.527

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=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AJAP1	NM_018836.4	c.29+1877A>G		intron_variant	Intron 1 of 5	ENST00000378191.5	NP_061324.1
AJAP1	NM_001042478.2	c.29+1877A>G		intron_variant	Intron 1 of 5		NP_001035943.1
AJAP1	XM_011541786.3	c.29+1877A>G		intron_variant	Intron 1 of 6		XP_011540088.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AJAP1	ENST00000378191.5	c.29+1877A>G		intron_variant	Intron 1 of 5	1	NM_018836.4	ENSP00000367433.3
AJAP1	ENST00000378190.7	c.29+1877A>G		intron_variant	Intron 1 of 5	5		ENSP00000367432.3

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25433 AN: 151126 Hom.: 2630 Cov.: 31

Gnomad AFR AF: 0.0493

Gnomad AMI AF: 0.0802

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.168 AC: 25425 AN: 151242 Hom.: 2628 Cov.: 31 AF XY: 0.174 AC XY: 12863 AN XY: 73852

African (AFR) AF: 0.0493 AC: 2027 AN: 41148

American (AMR) AF: 0.149 AC: 2267 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 613 AN: 3466

East Asian (EAS) AF: 0.296 AC: 1503 AN: 5086

South Asian (SAS) AF: 0.279 AC: 1334 AN: 4782

European-Finnish (FIN) AF: 0.286 AC: 2987 AN: 10428

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14279 AN: 67814

Other (OTH) AF: 0.143 AC: 299 AN: 2094

Alfa AF: 0.182 Hom.: 5585

Bravo AF: 0.148

Asia WGS AF: 0.263 AC: 915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	7.7
DANN	Benign	0.60
PhyloP100		0.53
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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Other links and lift over

dbSNP: rs1483198; hg19: chr1-4717391;