chr5-112644409-T-C

Variant names:

• chr5-112644409-T-C
• rs748628
• ENST00000690425.2:n.722+12312T>C

Variant summary

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

The ENST00000690425.2(LINC02200):​n.722+12312T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 152,082 control chromosomes in the GnomAD database, including 38,698 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 0.71 (38698 hom., cov: 31)
• Consequence: LINC02200 ENST00000690425.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.534
• Publications: 6 publications found

Genes affected

LINC02200 (HGNC:53066): (long intergenic non-protein coding RNA 2200)

ENSG00000300650 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02200	ENST00000690425.2	n.722+12312T>C		intron_variant	Intron 4 of 4
ENSG00000300650	ENST00000773182.1	n.223+13786A>G		intron_variant	Intron 2 of 2
ENSG00000300650	ENST00000773183.1	n.224-9358A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.711 AC: 107992 AN: 151964 Hom.: 38666 Cov.: 31

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.744

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.756

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.742

Gnomad OTH AF: 0.691

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

GnomAD4 genome AF: 0.711 AC: 108075 AN: 152082 Hom.: 38698 Cov.: 31 AF XY: 0.714 AC XY: 53101 AN XY: 74342

African (AFR) AF: 0.619 AC: 25669 AN: 41452

American (AMR) AF: 0.778 AC: 11892 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.784 AC: 2722 AN: 3472

East Asian (EAS) AF: 0.720 AC: 3721 AN: 5168

South Asian (SAS) AF: 0.687 AC: 3304 AN: 4806

European-Finnish (FIN) AF: 0.756 AC: 8004 AN: 10584

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.742 AC: 50428 AN: 67994

Other (OTH) AF: 0.690 AC: 1456 AN: 2110

Alfa AF: 0.732 Hom.: 72467

Bravo AF: 0.710

Asia WGS AF: 0.720 AC: 2503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.86
DANN	Benign	0.66
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs748628; hg19: chr5-111980106;