rs62534439

Variant names:

• chr9-37644722-C-T
• rs62534439
• ENST00000540557.1:n.*1135+48420G>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+21402C>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 152,180 control chromosomes in the GnomAD database, including 1,125 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 (1125 hom., cov: 32)
• Consequence: FRMPD1 NM_001371224.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.568
• Publications: 1 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.168 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+21402C>T		intron	N/A	NP_001358153.1	Q5SYB0-1
	FRMPD1	NM_001371225.1		c.-5+41383C>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+48420G>A		intron	N/A	ENSP00000457548.1

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17785 AN: 152062 Hom.: 1121 Cov.: 32

Gnomad AFR AF: 0.0888

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.0915

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.117 AC: 17795 AN: 152180 Hom.: 1125 Cov.: 32 AF XY: 0.118 AC XY: 8796 AN XY: 74406

African (AFR) AF: 0.0886 AC: 3678 AN: 41494

American (AMR) AF: 0.150 AC: 2288 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 473 AN: 3468

East Asian (EAS) AF: 0.177 AC: 920 AN: 5184

South Asian (SAS) AF: 0.163 AC: 786 AN: 4824

European-Finnish (FIN) AF: 0.0915 AC: 969 AN: 10588

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

European-Non Finnish (NFE) AF: 0.122 AC: 8311 AN: 68006

Other (OTH) AF: 0.135 AC: 285 AN: 2112

Alfa AF: 0.123 Hom.: 363

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	-0.82
CADD	Benign	5.9
DANN	Benign	0.60
PhyloP100		0.57

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: rs62534439; hg19: chr9-37644719;