chr9-37649693-A-G

Variant names:

• chr9-37649693-A-G
• rs62534444
• ENST00000540557.1:n.*1135+43449T>C

Variant summary

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

The ENST00000540557.1(ENSG00000255872):​n.*1135+43449T>C 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 152,206 control chromosomes in the GnomAD database, including 1,087 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 (1087 hom., cov: 32)
• Consequence: ENSG00000255872 ENST00000540557.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FRMPD1	NM_001371224.1	c.-5+26373A>G		intron_variant	Intron 2 of 16		NP_001358153.1
FRMPD1	NM_001371225.1	c.-4-42945A>G		intron_variant	Intron 1 of 15		NP_001358154.1
FRMPD1	XM_047423003.1	c.-5+26373A>G		intron_variant	Intron 2 of 16		XP_047278959.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000255872	ENST00000540557.1	n.*1135+43449T>C		intron_variant	Intron 11 of 11	5		ENSP00000457548.1

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17403 AN: 152086 Hom.: 1084 Cov.: 32

Gnomad AFR AF: 0.0798

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.0920

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.114 AC: 17408 AN: 152206 Hom.: 1087 Cov.: 32 AF XY: 0.116 AC XY: 8610 AN XY: 74418

African (AFR) AF: 0.0795 AC: 3301 AN: 41518

American (AMR) AF: 0.149 AC: 2274 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 455 AN: 3468

East Asian (EAS) AF: 0.180 AC: 930 AN: 5178

South Asian (SAS) AF: 0.162 AC: 780 AN: 4818

European-Finnish (FIN) AF: 0.0920 AC: 975 AN: 10602

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

European-Non Finnish (NFE) AF: 0.122 AC: 8328 AN: 68002

Other (OTH) AF: 0.133 AC: 281 AN: 2114

Alfa AF: 0.0598 Hom.: 51

Bravo AF: 0.116

Asia WGS AF: 0.171 AC: 595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	11
DANN	Benign	0.76
PhyloP100		-0.033

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: rs62534444; hg19: chr9-37649690;