chr4-189784978-C-T

Position:

• chr4-189784978-C-T

Variant summary

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

The XR_007058516.1(LOC124900882):​n.2109G>A 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 0.489 in 151,980 control chromosomes in the GnomAD database, including 18,970 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 0.49 (18970 hom., cov: 32)
• Consequence: LOC124900882 XR_007058516.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.811

Genes affected

LOC124900882 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124900882	XR_007058516.1	n.2109G>A		non_coding_transcript_exon_variant	2/2
FRG1-DT	NR_149039.1	n.1407-19231G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FRG1-DT	ENST00000660244.1	n.1407-19231G>A		intron_variant, non_coding_transcript_variant
FRG1-DT	ENST00000506276.5	n.240-4179G>A		intron_variant, non_coding_transcript_variant		3
FRG1-DT	ENST00000656003.1	n.668-19231G>A		intron_variant, non_coding_transcript_variant
FRG1-DT	ENST00000657714.1	n.757-19231G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74249 AN: 151860 Hom.: 18964 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.489 AC: 74296 AN: 151980 Hom.: 18970 Cov.: 32 AF XY: 0.490 AC XY: 36384 AN XY: 74290

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.816

Gnomad4 SAS AF: 0.548

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.522

Alfa AF: 0.515 Hom.: 15871

Bravo AF: 0.492

Asia WGS AF: 0.648 AC: 2251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.83
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1317423; hg19: chr4-190706132;