rs1915853

Positions:

• chr4-189868297-T-A
• chr4-189868297-T-C
• chr4-189868297-T-G

Variant summary

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

The NR_149039.1(FRG1-DT):​n.1213-3511A>T variant causes a intron, non coding transcript 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 NR_149039.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620

Genes affected

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=-0.97).
• 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/exons	MANE	UniProt
FRG1-DT	NR_149039.1	n.1213-3511A>T		intron_variant, non_coding_transcript_variant
FRG1-DT	NR_149038.1	n.1213-3511A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FRG1-DT	ENST00000660244.1	n.1213-3511A>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.666

Gnomad4 SAS AF: 0.707

Gnomad4 FIN AF: 0.682

Gnomad4 NFE AF: 0.660

Gnomad4 OTH AF: 0.621

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1915853; hg19: chr4-190789452;