rs62534443

Variant names:

• chr9-37649132-G-A
• rs62534443
• ENST00000540557.1:n.*1135+44010C>T

Variant summary

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

The ENST00000540557.1(ENSG00000255872):​n.*1135+44010C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,116 control chromosomes in the GnomAD database, including 1,085 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 0.11 (1085 hom., cov: 31)
• Consequence: ENSG00000255872 ENST00000540557.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000540557.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FRMPD1	NM_001371224.1		c.-5+25812G>A		intron	N/A	NP_001358153.1
	FRMPD1	NM_001371225.1		c.-4-43506G>A		intron	N/A	NP_001358154.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000255872	ENST00000540557.1	TSL:5	n.*1135+44010C>T		intron	N/A	ENSP00000457548.1

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17382 AN: 151998 Hom.: 1082 Cov.: 31

Gnomad AFR AF: 0.0798

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.0920

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.114 AC: 17387 AN: 152116 Hom.: 1085 Cov.: 31 AF XY: 0.116 AC XY: 8600 AN XY: 74358

African (AFR) AF: 0.0796 AC: 3301 AN: 41492

American (AMR) AF: 0.149 AC: 2271 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 456 AN: 3472

East Asian (EAS) AF: 0.179 AC: 929 AN: 5182

South Asian (SAS) AF: 0.162 AC: 778 AN: 4810

European-Finnish (FIN) AF: 0.0920 AC: 973 AN: 10574

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8317 AN: 67978

Other (OTH) AF: 0.132 AC: 278 AN: 2112

Alfa AF: 0.113 Hom.: 107

Bravo AF: 0.116

Asia WGS AF: 0.171 AC: 593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.6
DANN	Benign	0.72
PhyloP100		1.2

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: rs62534443; hg19: chr9-37649129;