rs13422767

Variant names:

• chr2-162243749-G-A
• rs13422767
• ENST00000493182.1:n.409-249C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-162243749-G-A
• chr2-162243749-G-T

Variant summary

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

The ENST00000493182.1(FAP):​n.409-249C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,110 control chromosomes in the GnomAD database, including 2,162 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 0.14 (2162 hom., cov: 33)
• Consequence: FAP ENST00000493182.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24
• Publications: 14 publications found

Genes affected

FAP (HGNC:3590): (fibroblast activation protein alpha) The protein encoded by this gene is a homodimeric integral membrane gelatinase belonging to the serine protease family. It is selectively expressed in reactive stromal fibroblasts of epithelial cancers, granulation tissue of healing wounds, and malignant cells of bone and soft tissue sarcomas. This protein is thought to be involved in the control of fibroblast growth or epithelial-mesenchymal interactions during development, tissue repair, and epithelial carcinogenesis. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2014]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAP	ENST00000493182.1	n.409-249C>T		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21510 AN: 151992 Hom.: 2167 Cov.: 33

Gnomad AFR AF: 0.0332

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.141 AC: 21487 AN: 152110 Hom.: 2162 Cov.: 33 AF XY: 0.146 AC XY: 10888 AN XY: 74364

African (AFR) AF: 0.0331 AC: 1374 AN: 41520

American (AMR) AF: 0.102 AC: 1558 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 433 AN: 3468

East Asian (EAS) AF: 0.294 AC: 1525 AN: 5184

South Asian (SAS) AF: 0.392 AC: 1891 AN: 4824

European-Finnish (FIN) AF: 0.197 AC: 2080 AN: 10558

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12063 AN: 67956

Other (OTH) AF: 0.135 AC: 285 AN: 2114

Alfa AF: 0.151 Hom.: 983

Bravo AF: 0.124

Asia WGS AF: 0.314 AC: 1094 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.8
DANN	Benign	0.64
PhyloP100		1.2
PromoterAI		0.0052	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs13422767; hg19: chr2-163100259;