rs169439

Variant names:

• chr10-48242632-C-A
• rs169439
• NM_001018071.4:c.376-280G>T

Your query was ambiguous. Multiple possible variants found:

• chr10-48242632-C-A
• chr10-48242632-C-G

Variant summary

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

The NM_001018071.4(FRMPD2):​c.376-280G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.824 in 152,262 control chromosomes in the GnomAD database, including 54,747 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 0.82 (54747 hom., cov: 34)
• Consequence: FRMPD2 NM_001018071.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.734
• Publications: 4 publications found

Genes affected

FRMPD2 (HGNC:28572): (FERM and PDZ domain containing 2) This gene encodes a peripheral membrane protein and is located in a region of chromosome 10q that contains a segmental duplication. This copy of the gene is full-length and is in the telomeric duplicated region. Two other more centromerically proximal copies of the gene are partial and may represent pseudogenes. This full-length gene appears to function in the establishment and maintenance of cell polarization. The protein is recruited to cell-cell junctions in an E-cadherin-dependent manner, and is selectively localized at the basolateral membrane in polarized epithelial cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2009]

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 (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FRMPD2	NM_001018071.4	c.376-280G>T		intron_variant	Intron 4 of 28	ENST00000374201.8	NP_001018081.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FRMPD2	ENST00000374201.8	c.376-280G>T		intron_variant	Intron 4 of 28	1	NM_001018071.4	ENSP00000363317.3

Frequencies

GnomAD3 genomes AF: 0.824 AC: 125403 AN: 152144 Hom.: 54719 Cov.: 34

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.967

Gnomad AMR AF: 0.917

Gnomad ASJ AF: 0.891

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.956

Gnomad FIN AF: 0.952

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.948

Gnomad OTH AF: 0.863

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

GnomAD4 genome AF: 0.824 AC: 125479 AN: 152262 Hom.: 54747 Cov.: 34 AF XY: 0.831 AC XY: 61863 AN XY: 74460

African (AFR) AF: 0.505 AC: 20957 AN: 41502

American (AMR) AF: 0.917 AC: 14045 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.891 AC: 3093 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5171 AN: 5176

South Asian (SAS) AF: 0.957 AC: 4624 AN: 4830

European-Finnish (FIN) AF: 0.952 AC: 10121 AN: 10628

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.948 AC: 64486 AN: 68024

Other (OTH) AF: 0.865 AC: 1831 AN: 2116

Alfa AF: 0.913 Hom.: 108565

Bravo AF: 0.805

Asia WGS AF: 0.958 AC: 3331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.39
DANN	Benign	0.36
PhyloP100		-0.73
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: rs169439; hg19: chr10-49450675;