rs2182317

Variant names:

• chr9-37641854-G-T
• rs2182317
• ENST00000540557.1:n.*1135+51288C>A

Variant summary

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

The NM_001371224.1(FRMPD1):​c.-5+18534G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,152 control chromosomes in the GnomAD database, including 1,132 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 0.12 (1132 hom., cov: 32)
• Consequence: FRMPD1 NM_001371224.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.603
• Publications: 6 publications found

Genes affected

ENSG00000255872 (HGNC:):

FRMPD1 (HGNC:29159): (FERM and PDZ domain containing 1) Involved in establishment of protein localization to membrane and regulation of G protein-coupled receptor signaling pathway. Located in plasma membrane. Part of protein-containing complex. Colocalizes with cell cortex. [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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001371224.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FRMPD1	NM_001371224.1		c.-5+18534G>T		intron	N/A	NP_001358153.1	Q5SYB0-1
	FRMPD1	NM_001371225.1		c.-5+38515G>T		intron	N/A	NP_001358154.1	Q5SYB0-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000255872	ENST00000540557.1	TSL:5	n.*1135+51288C>A		intron	N/A	ENSP00000457548.1

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17799 AN: 152032 Hom.: 1128 Cov.: 32

Gnomad AFR AF: 0.0891

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.0921

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.117 AC: 17809 AN: 152152 Hom.: 1132 Cov.: 32 AF XY: 0.118 AC XY: 8800 AN XY: 74380

African (AFR) AF: 0.0890 AC: 3693 AN: 41512

American (AMR) AF: 0.150 AC: 2285 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 459 AN: 3472

East Asian (EAS) AF: 0.176 AC: 913 AN: 5180

South Asian (SAS) AF: 0.163 AC: 787 AN: 4820

European-Finnish (FIN) AF: 0.0921 AC: 976 AN: 10594

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8325 AN: 67982

Other (OTH) AF: 0.136 AC: 286 AN: 2106

Alfa AF: 0.125 Hom.: 693

Bravo AF: 0.119

Asia WGS AF: 0.174 AC: 603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.23
DANN	Benign	0.70
PhyloP100		-0.60

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: rs2182317; hg19: chr9-37641851;