rs6844114

Variant names:

• chr4-189824738-G-A
• rs6844114
• ENST00000506276.5:n.240-43939C>T

Variant summary

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

The ENST00000506276.5(FRG1-DT):​n.240-43939C>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 ENST00000506276.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267
• Publications: 4 publications found

Genes affected

FRG1-DT (HGNC:51590): (FRG1 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000506276.5. 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
	FRG1-DT	NR_149039.1		n.1406+39855C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FRG1-DT	ENST00000506276.5	TSL:3	n.240-43939C>T		intron	N/A
	FRG1-DT	ENST00000508156.6	TSL:3	n.857-3073C>T		intron	N/A
	FRG1-DT	ENST00000511785.3	TSL:2	n.696-3073C>T		intron	N/A

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

African (AFR) AF: 0.343 AC: 14201 AN: 41442

American (AMR) AF: 0.139 AC: 2124 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0542 AC: 188 AN: 3470

East Asian (EAS) AF: 0.0749 AC: 387 AN: 5166

South Asian (SAS) AF: 0.172 AC: 830 AN: 4816

European-Finnish (FIN) AF: 0.0561 AC: 595 AN: 10604

Middle Eastern (MID) AF: 0.0959 AC: 28 AN: 292

European-Non Finnish (NFE) AF: 0.0887 AC: 6030 AN: 68000

Other (OTH) AF: 0.137 AC: 290 AN: 2116

Alfa AF: 0.114 Hom.: 5175

Bravo AF: 0.174

Asia WGS AF: 0.145 AC: 506 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.0
DANN	Benign	0.49
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs6844114; hg19: chr4-190745892;