9-83219828-G-T

Variant names:

• chr9-83219828-G-T
• rs12237222
• ENST00000798705.1:n.33C>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000798705.1(ENSG00000303992):​n.33C>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 0.545 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: ENSG00000303992 ENST00000798705.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.10
• Publications: 9 publications found

Genes affected

ENSG00000303992 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FRMD3-AS1	NR_184120.1	n.33+451G>T		intron_variant	Intron 1 of 2
FRMD3-AS1	NR_184121.1	n.33+451G>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303992	ENST00000798705.1	n.33C>A		non_coding_transcript_exon_variant	Exon 1 of 4
FRMD3-AS1	ENST00000416473.3	n.97+451G>T		intron_variant	Intron 1 of 2	2
FRMD3-AS1	ENST00000662757.2	n.96+451G>T		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.459 AC: 19061 AN: 41506

American (AMR) AF: 0.512 AC: 7829 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 2260 AN: 3472

East Asian (EAS) AF: 0.779 AC: 4010 AN: 5150

South Asian (SAS) AF: 0.709 AC: 3423 AN: 4830

European-Finnish (FIN) AF: 0.507 AC: 5369 AN: 10582

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.576 AC: 39155 AN: 67984

Other (OTH) AF: 0.542 AC: 1145 AN: 2112

Alfa AF: 0.559 Hom.: 31856

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
PhyloP100		3.1

Splicing

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

Other links and lift over

dbSNP: rs12237222; hg19: chr9-85834743;