rs12237222

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr9-83219828-G-A
• chr9-83219828-G-C
• chr9-83219828-G-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The ENST00000798705.1(ENSG00000303992):​n.33C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FRMD3-AS1	NR_184120.1	n.33+451G>A		intron_variant	Intron 1 of 2
FRMD3-AS1	NR_184121.1	n.33+451G>A		intron_variant	Intron 1 of 1

Ensembl

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

Frequencies

GnomAD3 genomes Cov.: 34

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

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
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;