4-189786276-C-G

Position:

• chr4-189786276-C-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC124900882 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124900882	XR_007058516.1	n.811G>C		non_coding_transcript_exon_variant	2/2
FRG1-DT	NR_149039.1	n.1407-20529G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FRG1-DT	ENST00000506276.5	n.240-5477G>C		intron_variant		3
FRG1-DT	ENST00000656003.1	n.668-20529G>C		intron_variant
FRG1-DT	ENST00000657714.1	n.757-20529G>C		intron_variant
FRG1-DT	ENST00000660244.1	n.1407-20529G>C		intron_variant

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

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.703

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.925

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.700

Gnomad4 NFE AF: 0.715

Gnomad4 OTH AF: 0.628

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2739532; hg19: chr4-190707430;