rs7700025

Positions:

• chr4-176893709-G-A
• chr4-176893709-G-C
• chr4-176893709-G-T

Variant summary

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

The ENST00000656694.1(ENSG00000287544):​n.384+159C>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 0.604 in 151,868 control chromosomes in the GnomAD database, including 29,113 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 0.60 (29113 hom., cov: 32)
• Consequence: ENST00000656694.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.219

Genes affected

(HGNC:):

LINC02509 (HGNC:53498): (long intergenic non-protein coding RNA 2509)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000656694.1	n.384+159C>T		intron_variant, non_coding_transcript_variant
LINC02509	ENST00000670563.1	n.351+11281G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.604 AC: 91627 AN: 151750 Hom.: 29097 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.710

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.722

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.604 AC: 91687 AN: 151868 Hom.: 29113 Cov.: 32 AF XY: 0.603 AC XY: 44768 AN XY: 74202

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.630

Gnomad4 ASJ AF: 0.722

Gnomad4 EAS AF: 0.631

Gnomad4 SAS AF: 0.613

Gnomad4 FIN AF: 0.717

Gnomad4 NFE AF: 0.700

Gnomad4 OTH AF: 0.630

Alfa AF: 0.684 Hom.: 57534

Bravo AF: 0.588

Asia WGS AF: 0.586 AC: 2040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7700025; hg19: chr4-177814863;