rs6844114

Positions:

• chr4-189824738-G-A

Variant summary

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

The ENST00000511785.2(FRG1-DT):​n.426-3073C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,106 control chromosomes in the GnomAD database, including 3,040 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 0.16 (3040 hom., cov: 32)
• Consequence: FRG1-DT ENST00000511785.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267

Genes affected

FRG1-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FRG1-DT	NR_149039.1	n.1406+39855C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FRG1-DT	ENST00000506276.5	n.240-43939C>T		intron_variant		3
FRG1-DT	ENST00000508156.5	n.333-3073C>T		intron_variant		3
FRG1-DT	ENST00000511785.2	n.426-3073C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24720 AN: 151990 Hom.: 3037 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.0857

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.0542

Gnomad EAS AF: 0.0753

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.0561

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0887

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.163 AC: 24751 AN: 152106 Hom.: 3040 Cov.: 32 AF XY: 0.160 AC XY: 11884 AN XY: 74366

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.0542

Gnomad4 EAS AF: 0.0749

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.0561

Gnomad4 NFE AF: 0.0887

Gnomad4 OTH AF: 0.137

Alfa AF: 0.100 Hom.: 1464

Bravo AF: 0.174

Asia WGS AF: 0.145 AC: 506 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.0
DANN	Benign	0.49

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6844114; hg19: chr4-190745892;