chr22-44572650-G-C

Variant names:

• chr22-44572650-G-C
• rs138597
• ENST00000603530.6:n.*206G>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000603530.6(LINC00207):​n.*206G>C variant causes a downstream gene 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: 29)
• Consequence: LINC00207 ENST00000603530.6 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.192
• Publications: 6 publications found

Genes affected

LINC00207 (HGNC:37255): (long intergenic non-protein coding RNA 207)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00207	NR_028409.1	n.*201G>C		downstream_gene_variant
LINC00207	NR_028410.1	n.*201G>C		downstream_gene_variant
LINC00207	NR_028411.1	n.*201G>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00207	ENST00000603530.6	n.*206G>C		downstream_gene_variant		1
LINC00207	ENST00000334566.10	n.*197G>C		downstream_gene_variant		5
LINC00207	ENST00000657777.2	n.*197G>C		downstream_gene_variant

Frequencies

GnomAD3 genomes Cov.: 29

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

GnomAD4 genome Cov.: 29

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.83
DANN	Benign	0.75
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs138597; hg19: chr22-44968530;