2-178471873-T-C

Variant names:

• chr2-178471873-T-C
• rs17225700
• NM_181342.3:c.374-2088A>G

Variant summary

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

The NM_181342.3(FKBP7):​c.374-2088A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0585 in 152,220 control chromosomes in the GnomAD database, including 336 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 0.058 (336 hom., cov: 32)
• Consequence: FKBP7 NM_181342.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.285
• Publications: 4 publications found

Genes affected

FKBP7 (HGNC:3723): (FKBP prolyl isomerase 7) The protein encoded by this gene belongs to the FKBP-type peptidyl-prolyl cis/trans isomerase (PPIase) family. Members of this family exhibit PPIase activity and function as molecular chaperones. A similar protein in mouse is located in the endoplasmic reticulum and binds calcium. [provided by RefSeq, Jul 2008]

LOC124906102 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0819 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FKBP7	NM_181342.3	c.374-2088A>G		intron_variant	Intron 2 of 3	ENST00000424785.7	NP_851939.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FKBP7	ENST00000424785.7	c.374-2088A>G		intron_variant	Intron 2 of 3	1	NM_181342.3	ENSP00000413152.2

Frequencies

GnomAD3 genomes AF: 0.0585 AC: 8899 AN: 152102 Hom.: 336 Cov.: 32

Gnomad AFR AF: 0.0275

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0539

Gnomad ASJ AF: 0.0524

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0215

Gnomad FIN AF: 0.0740

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0837

Gnomad OTH AF: 0.0528

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

GnomAD4 genome AF: 0.0585 AC: 8898 AN: 152220 Hom.: 336 Cov.: 32 AF XY: 0.0570 AC XY: 4244 AN XY: 74412

African (AFR) AF: 0.0275 AC: 1143 AN: 41544

American (AMR) AF: 0.0539 AC: 824 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0524 AC: 182 AN: 3472

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5184

South Asian (SAS) AF: 0.0213 AC: 102 AN: 4786

European-Finnish (FIN) AF: 0.0740 AC: 785 AN: 10608

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0837 AC: 5692 AN: 68016

Other (OTH) AF: 0.0522 AC: 110 AN: 2106

Alfa AF: 0.0721 Hom.: 443

Bravo AF: 0.0547

Asia WGS AF: 0.00809 AC: 29 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.9
DANN	Benign	0.71
PhyloP100		-0.28
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

Other links and lift over

dbSNP: rs17225700; hg19: chr2-179336600;