22-44572650-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000603530.6(LINC00207):​n.*206G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 151,730 control chromosomes in the GnomAD database, including 28,632 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 0.59 (28632 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000603530.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00207	NR_028409.1		n.*201G>A		downstream_gene	N/A
	LINC00207	NR_028410.1		n.*201G>A		downstream_gene	N/A
	LINC00207	NR_028411.1		n.*201G>A		downstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00207	ENST00000603530.6	TSL:1	n.*206G>A		downstream_gene	N/A
	LINC00207	ENST00000334566.10	TSL:5	n.*197G>A		downstream_gene	N/A
	LINC00207	ENST00000657777.2		n.*197G>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89279 AN: 151612 Hom.: 28632 Cov.: 29

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.670

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.588 AC: 89293 AN: 151730 Hom.: 28632 Cov.: 29 AF XY: 0.592 AC XY: 43827 AN XY: 74086

African (AFR) AF: 0.317 AC: 13119 AN: 41414

American (AMR) AF: 0.641 AC: 9768 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.786 AC: 2726 AN: 3466

East Asian (EAS) AF: 0.509 AC: 2596 AN: 5102

South Asian (SAS) AF: 0.665 AC: 3178 AN: 4776

European-Finnish (FIN) AF: 0.693 AC: 7298 AN: 10538

Middle Eastern (MID) AF: 0.669 AC: 194 AN: 290

European-Non Finnish (NFE) AF: 0.715 AC: 48532 AN: 67884

Other (OTH) AF: 0.638 AC: 1344 AN: 2106

Alfa AF: 0.677 Hom.: 110551

Bravo AF: 0.576

Asia WGS AF: 0.553 AC: 1924 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.76
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;