ENST00000577004.3:n.749+6527C>G

Variant names:

• chr13-22909191-G-C
• rs971206
• ENST00000577004.3:n.749+6527C>G

Variant summary

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

The ENST00000577004.3(LINC00621):​n.749+6527C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.806 in 152,100 control chromosomes in the GnomAD database, including 50,255 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 0.81 (50255 hom., cov: 31)
• Consequence: LINC00621 ENST00000577004.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.817
• Publications: 2 publications found

Genes affected

LINC00621 (HGNC:44227): (long intergenic non-protein coding RNA 621)

ENSG00000262198 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000577004.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00621	NR_138043.1		n.652+6527C>G		intron	N/A
	LOC105370109	NR_187640.1		n.*132G>C		downstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00621	ENST00000577004.3	TSL:4	n.749+6527C>G		intron	N/A
	LINC00621	ENST00000658532.1		n.229+6527C>G		intron	N/A
	LINC00621	ENST00000663150.1		n.50+6527C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122452 AN: 151982 Hom.: 50235 Cov.: 31

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.828

Gnomad AMR AF: 0.862

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.861

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.930

Gnomad MID AF: 0.771

Gnomad NFE AF: 0.871

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.806 AC: 122521 AN: 152100 Hom.: 50255 Cov.: 31 AF XY: 0.811 AC XY: 60295 AN XY: 74382

African (AFR) AF: 0.631 AC: 26132 AN: 41442

American (AMR) AF: 0.863 AC: 13193 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.825 AC: 2864 AN: 3472

East Asian (EAS) AF: 0.862 AC: 4442 AN: 5156

South Asian (SAS) AF: 0.855 AC: 4121 AN: 4818

European-Finnish (FIN) AF: 0.930 AC: 9867 AN: 10606

Middle Eastern (MID) AF: 0.760 AC: 222 AN: 292

European-Non Finnish (NFE) AF: 0.871 AC: 59219 AN: 67994

Other (OTH) AF: 0.808 AC: 1706 AN: 2112

Alfa AF: 0.831 Hom.: 6596

Bravo AF: 0.793

Asia WGS AF: 0.845 AC: 2937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.55
DANN	Benign	0.45
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs971206; hg19: chr13-23483330;