rs7664420

Positions:

• chr4-137050598-G-A

Variant summary

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

The NR_149105.1(LINC02511):​n.103+38963C>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 0.91 in 152,194 control chromosomes in the GnomAD database, including 63,565 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 0.91 (63565 hom., cov: 32)
• Consequence: LINC02511 NR_149105.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.285

Genes affected

LINC02511 (HGNC:53500): (long intergenic non-protein coding RNA 2511)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.978 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02511	NR_149105.1	n.103+38963C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02511	ENST00000656956.1	n.77+38963C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.910 AC: 138340 AN: 152078 Hom.: 63526 Cov.: 32

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.986

Gnomad AMR AF: 0.905

Gnomad ASJ AF: 0.963

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.912

Gnomad FIN AF: 0.936

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.984

Gnomad OTH AF: 0.915

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

GnomAD4 genome AF: 0.910 AC: 138431 AN: 152194 Hom.: 63565 Cov.: 32 AF XY: 0.908 AC XY: 67562 AN XY: 74432

Gnomad4 AFR AF: 0.789

Gnomad4 AMR AF: 0.905

Gnomad4 ASJ AF: 0.963

Gnomad4 EAS AF: 0.797

Gnomad4 SAS AF: 0.912

Gnomad4 FIN AF: 0.936

Gnomad4 NFE AF: 0.984

Gnomad4 OTH AF: 0.915

Alfa AF: 0.940 Hom.: 8545

Bravo AF: 0.901

Asia WGS AF: 0.847 AC: 2947 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.51
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7664420; hg19: chr4-137971752;