rs11728249

Variant names:

• chr4-82620172-G-A
• rs11728249
• ENST00000426551.5:n.226+1040C>T

Variant summary

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

The ENST00000426551.5(LINC00575):​n.226+1040C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0407 in 152,284 control chromosomes in the GnomAD database, including 202 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 0.041 (202 hom., cov: 32)
• Consequence: LINC00575 ENST00000426551.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.716
• Publications: 1 publications found

Genes affected

LINC00575 (HGNC:21342): (long intergenic non-protein coding RNA 575)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.053 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000426551.5. 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
	LINC00575	NR_024087.1		n.226+1040C>T		intron	N/A
	LINC00575	NR_024088.1		n.226+1040C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00575	ENST00000426551.5	TSL:1	n.226+1040C>T		intron	N/A
	LINC00575	ENST00000515811.1	TSL:1	n.226+1040C>T		intron	N/A
	LINC00575	ENST00000651054.1		n.399+1040C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0407 AC: 6195 AN: 152166 Hom.: 202 Cov.: 32

Gnomad AFR AF: 0.00893

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.0330

Gnomad ASJ AF: 0.0366

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0363

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0545

Gnomad OTH AF: 0.0464

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

GnomAD4 genome AF: 0.0407 AC: 6193 AN: 152284 Hom.: 202 Cov.: 32 AF XY: 0.0433 AC XY: 3221 AN XY: 74454

African (AFR) AF: 0.00890 AC: 370 AN: 41558

American (AMR) AF: 0.0329 AC: 504 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0366 AC: 127 AN: 3470

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5186

South Asian (SAS) AF: 0.0359 AC: 173 AN: 4822

European-Finnish (FIN) AF: 0.103 AC: 1091 AN: 10604

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0545 AC: 3707 AN: 68024

Other (OTH) AF: 0.0459 AC: 97 AN: 2114

Alfa AF: 0.0502 Hom.: 282

Bravo AF: 0.0351

Asia WGS AF: 0.0130 AC: 45 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.2
DANN	Benign	0.43
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs11728249; hg19: chr4-83541325;