chr9-37711597-A-C

Variant names:

• chr9-37711597-A-C
• rs2296553
• NM_014907.3:c.408+202A>C

Variant summary

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

The NM_014907.3(FRMPD1):​c.408+202A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 151,954 control chromosomes in the GnomAD database, including 13,238 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 0.42 (13238 hom., cov: 32)
• Consequence: FRMPD1 NM_014907.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206
• Publications: 5 publications found

Genes affected

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]

ENSG00000255872 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014907.3. 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_014907.3	MANE Select	c.408+202A>C		intron	N/A	NP_055722.2
	FRMPD1	NM_001371223.1		c.408+202A>C		intron	N/A	NP_001358152.1
	FRMPD1	NM_001371224.1		c.408+202A>C		intron	N/A	NP_001358153.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FRMPD1	ENST00000377765.8	TSL:1 MANE Select	c.408+202A>C		intron	N/A	ENSP00000366995.3
	FRMPD1	ENST00000539465.5	TSL:1	c.408+202A>C		intron	N/A	ENSP00000444411.1
	ENSG00000255872	ENST00000540557.1	TSL:5	n.*1011+16331T>G		intron	N/A	ENSP00000457548.1

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63239 AN: 151836 Hom.: 13227 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.416 AC: 63285 AN: 151954 Hom.: 13238 Cov.: 32 AF XY: 0.415 AC XY: 30782 AN XY: 74256

African (AFR) AF: 0.373 AC: 15461 AN: 41470

American (AMR) AF: 0.391 AC: 5966 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1494 AN: 3470

East Asian (EAS) AF: 0.564 AC: 2912 AN: 5162

South Asian (SAS) AF: 0.317 AC: 1527 AN: 4810

European-Finnish (FIN) AF: 0.449 AC: 4719 AN: 10510

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29867 AN: 67956

Other (OTH) AF: 0.439 AC: 926 AN: 2110

Alfa AF: 0.428 Hom.: 23791

Bravo AF: 0.413

Asia WGS AF: 0.430 AC: 1500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.3
DANN	Benign	0.74
PhyloP100		-0.21
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: rs2296553; hg19: chr9-37711594;