2-162214651-C-G

Position:

• chr2-162214651-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004460.5(FAP):​c.867-578G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0361 in 150,378 control chromosomes in the GnomAD database, including 465 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 0.036 (465 hom., cov: 32)
• Consequence: FAP NM_004460.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAP	NM_004460.5	c.867-578G>C		intron_variant		ENST00000188790.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAP	ENST00000188790.9	c.867-578G>C		intron_variant		1	NM_004460.5	P1
FAP	ENST00000480838.1	n.854-578G>C		intron_variant, non_coding_transcript_variant		1
FAP	ENST00000443424.5	c.792-578G>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0358 AC: 5383 AN: 150260 Hom.: 449 Cov.: 32

Gnomad AFR AF: 0.0105

Gnomad AMI AF: 0.00993

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.00578

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.0200

Gnomad FIN AF: 0.0122

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0121

Gnomad OTH AF: 0.0455

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

GnomAD4 genome AF: 0.0361 AC: 5425 AN: 150378 Hom.: 465 Cov.: 32 AF XY: 0.0390 AC XY: 2860 AN XY: 73284

Gnomad4 AFR AF: 0.0107

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.00578

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.0204

Gnomad4 FIN AF: 0.0122

Gnomad4 NFE AF: 0.0121

Gnomad4 OTH AF: 0.0527

Alfa AF: 0.0269 Hom.: 34

Bravo AF: 0.0547

Asia WGS AF: 0.112 AC: 388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.1
DANN	Benign	0.44

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs4664454; hg19: chr2-163071161;