rs11728249

chr4-82620172-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_024088.1(LINC00575):n.226+1040C>T variant causes a intron, non coding transcript 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 NR_024088.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.716

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00575	NR_024088.1	n.226+1040C>T		intron_variant, non_coding_transcript_variant
LINC00575	NR_024087.1	n.226+1040C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00575	ENST00000426551.5	n.226+1040C>T		intron_variant, non_coding_transcript_variant		1
LINC00575	ENST00000515811.1	n.226+1040C>T		intron_variant, non_coding_transcript_variant		1
LINC00575	ENST00000651054.1	n.399+1040C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.00890

Gnomad4 AMR AF: 0.0329

Gnomad4 ASJ AF: 0.0366

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0359

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.0545

Gnomad4 OTH AF: 0.0459

Alfa AF: 0.0424 Hom.: 24

Bravo AF: 0.0351

Asia WGS AF: 0.0130 AC: 45 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	4.2
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11728249; hg19: chr4-83541325;