rs62534439

Positions:

• chr9-37644722-C-T

Variant summary

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

The NM_001371224.1(FRMPD1):​c.-5+21402C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,180 control chromosomes in the GnomAD database, including 1,125 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 0.12 (1125 hom., cov: 32)
• Consequence: FRMPD1 NM_001371224.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.568

Genes affected

FRMPD1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FRMPD1	NM_001371224.1	c.-5+21402C>T		intron_variant
FRMPD1	NM_001371225.1	c.-5+41383C>T		intron_variant
FRMPD1	XM_047423003.1	c.-5+21402C>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17785 AN: 152062 Hom.: 1121 Cov.: 32

Gnomad AFR AF: 0.0888

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.0915

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.117 AC: 17795 AN: 152180 Hom.: 1125 Cov.: 32 AF XY: 0.118 AC XY: 8796 AN XY: 74406

Gnomad4 AFR AF: 0.0886

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.0915

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.135

Alfa AF: 0.117 Hom.: 146

Bravo AF: 0.119

Asia WGS AF: 0.174 AC: 603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.9
DANN	Benign	0.60

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: rs62534439; hg19: chr9-37644719;