9-83219828-G-T

Position:

• chr9-83219828-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_184120.1(FRMD3-AS1):​n.33+451G>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 0.545 in 152,132 control chromosomes in the GnomAD database, including 22,972 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 0.55 (22972 hom., cov: 34)
• Consequence: FRMD3-AS1 NR_184120.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.10

Genes affected

FRMD3-AS1 (HGNC:55790): (FRMD3 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FRMD3-AS1	NR_184120.1	n.33+451G>T		intron_variant, non_coding_transcript_variant
FRMD3-AS1	NR_184121.1	n.33+451G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FRMD3-AS1	ENST00000668931.1	n.43+451G>T		intron_variant, non_coding_transcript_variant
FRMD3-AS1	ENST00000416473.2	n.77+451G>T		intron_variant, non_coding_transcript_variant		2
FRMD3-AS1	ENST00000662757.1	n.90+451G>T		intron_variant, non_coding_transcript_variant
FRMD3-AS1	ENST00000665291.1	n.47+451G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82899 AN: 152014 Hom.: 22973 Cov.: 34

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.545 AC: 82928 AN: 152132 Hom.: 22972 Cov.: 34 AF XY: 0.546 AC XY: 40590 AN XY: 74378

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.651

Gnomad4 EAS AF: 0.779

Gnomad4 SAS AF: 0.709

Gnomad4 FIN AF: 0.507

Gnomad4 NFE AF: 0.576

Gnomad4 OTH AF: 0.542

Alfa AF: 0.503 Hom.: 3141

Bravo AF: 0.538

Asia WGS AF: 0.659 AC: 2296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	19
DANN	Uncertain	0.98

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12237222; hg19: chr9-85834743;