rs62534444

chr9-37649693-A-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+26373A>G 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: FRMPD1 NM_001371224.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330

Genes affected

FRMPD1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
FRMPD1	NM_001371224.1	c.-5+26373A>G		intron_variant
FRMPD1	NM_001371225.1	c.-4-42945A>G		intron_variant
FRMPD1	XM_047423003.1	c.-5+26373A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.0795

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.180

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.0920

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.133

Alfa AF: 0.0583 Hom.: 47

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

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: rs62534444; hg19: chr9-37649690;