chr9-37648370-C-G

Position:

• chr9-37648370-C-G

Variant summary

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

The NM_001371224.1(FRMPD1):​c.-5+25050C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.598 in 151,926 control chromosomes in the GnomAD database, including 28,265 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 0.60 (28265 hom., cov: 31)
• Consequence: FRMPD1 NM_001371224.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FRMPD1	NM_001371224.1	c.-5+25050C>G		intron_variant			NP_001358153.1
FRMPD1	NM_001371225.1	c.-4-44268C>G		intron_variant			NP_001358154.1
FRMPD1	XM_047423003.1	c.-5+25050C>G		intron_variant			XP_047278959.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000255872	ENST00000540557.1	n.*1135+44772G>C		intron_variant		5		ENSP00000457548.1

Frequencies

GnomAD3 genomes AF: 0.598 AC: 90763 AN: 151808 Hom.: 28241 Cov.: 31

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.598 AC: 90833 AN: 151926 Hom.: 28265 Cov.: 31 AF XY: 0.597 AC XY: 44326 AN XY: 74226

Gnomad4 AFR AF: 0.771

Gnomad4 AMR AF: 0.593

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.715

Gnomad4 SAS AF: 0.639

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.506

Gnomad4 OTH AF: 0.601

Alfa AF: 0.364 Hom.: 783

Bravo AF: 0.612

Asia WGS AF: 0.656 AC: 2282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.96
DANN	Benign	0.31

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

Publications

LitVar

Other links and lift over

dbSNP: rs2381718; hg19: chr9-37648367; COSMIC: COSV66702529;