4-189868297-T-A

Variant names:

• chr4-189868297-T-A
• rs1915853
• ENST00000501825.2:n.317-3511A>T

Variant summary

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

The ENST00000501825.2(FRG1-DT):​n.317-3511A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.642 in 152,166 control chromosomes in the GnomAD database, including 31,645 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 0.64 (31645 hom., cov: 34)
• Consequence: FRG1-DT ENST00000501825.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FRG1-DT	NR_149038.1	n.1213-3511A>T		intron_variant	Intron 2 of 2
FRG1-DT	NR_149039.1	n.1213-3511A>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FRG1-DT	ENST00000501825.2	n.317-3511A>T		intron_variant	Intron 2 of 2	1
FRG1-DT	ENST00000506276.5	n.239+68900A>T		intron_variant	Intron 2 of 2	3
FRG1-DT	ENST00000508156.6	n.856+27235A>T		intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97643 AN: 152048 Hom.: 31608 Cov.: 34

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.642 AC: 97732 AN: 152166 Hom.: 31645 Cov.: 34 AF XY: 0.645 AC XY: 47952 AN XY: 74382

African (AFR) AF: 0.578 AC: 24002 AN: 41514

American (AMR) AF: 0.710 AC: 10862 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 2037 AN: 3470

East Asian (EAS) AF: 0.666 AC: 3437 AN: 5164

South Asian (SAS) AF: 0.707 AC: 3412 AN: 4828

European-Finnish (FIN) AF: 0.682 AC: 7215 AN: 10576

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.660 AC: 44857 AN: 68000

Other (OTH) AF: 0.621 AC: 1312 AN: 2112

Alfa AF: 0.574 Hom.: 1708

Bravo AF: 0.640

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.5
DANN	Benign	0.14
PhyloP100		0.062

Splicing

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

Other links and lift over

dbSNP: rs1915853; hg19: chr4-190789452;