rs6958639

chr7-106819471-G-A

Variant summary

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

The ENST00000490162.3(LINC02577):n.184-3593G>A 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 0.263 in 152,122 control chromosomes in the GnomAD database, including 5,703 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 0.26 (5703 hom., cov: 32)
• Consequence: LINC02577 ENST00000490162.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71

Genes affected

LINC02577 (HGNC:53749): (long intergenic non-protein coding RNA 2577)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02577	NR_170302.1	n.160-3593G>A		intron_variant, non_coding_transcript_variant
LINC02577	NR_170303.1	n.160-3593G>A		intron_variant, non_coding_transcript_variant
LINC02577	NR_170304.1	n.160-3593G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02577	ENST00000490162.3	n.184-3593G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39964 AN: 152004 Hom.: 5707 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.00539

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.263 AC: 39968 AN: 152122 Hom.: 5703 Cov.: 32 AF XY: 0.254 AC XY: 18880 AN XY: 74368

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.246

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.00541

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.265

Alfa AF: 0.313 Hom.: 12041

Bravo AF: 0.263

Asia WGS AF: 0.0940 AC: 331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.42
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6958639; hg19: chr7-106459917;