4-189786276-C-G

Variant names:

• chr4-189786276-C-G
• rs2739532
• XR_007058516.1:n.811G>C

Variant summary

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

The XR_007058516.1(LOC124900882):​n.811G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.592 in 152,094 control chromosomes in the GnomAD database, including 29,732 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 0.59 (29732 hom., cov: 33)
• Consequence: LOC124900882 XR_007058516.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.439
• Publications: 1 publications found

Genes affected

LOC124900882 (HGNC:):

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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.903 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FRG1-DT	NR_149039.1		n.1407-20529G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FRG1-DT	ENST00000506276.5	TSL:3	n.240-5477G>C		intron	N/A
	FRG1-DT	ENST00000656003.2		n.668-20529G>C		intron	N/A
	FRG1-DT	ENST00000657714.1		n.757-20529G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.592 AC: 90012 AN: 151976 Hom.: 29732 Cov.: 33

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.592 AC: 90025 AN: 152094 Hom.: 29732 Cov.: 33 AF XY: 0.594 AC XY: 44192 AN XY: 74372

African (AFR) AF: 0.272 AC: 11290 AN: 41474

American (AMR) AF: 0.703 AC: 10751 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1797 AN: 3468

East Asian (EAS) AF: 0.925 AC: 4778 AN: 5164

South Asian (SAS) AF: 0.672 AC: 3230 AN: 4808

European-Finnish (FIN) AF: 0.700 AC: 7412 AN: 10590

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.715 AC: 48619 AN: 67980

Other (OTH) AF: 0.628 AC: 1329 AN: 2116

Alfa AF: 0.634 Hom.: 4066

Bravo AF: 0.577

Asia WGS AF: 0.731 AC: 2541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.3
DANN	Benign	0.31
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs2739532; hg19: chr4-190707430;