rs7700025

Variant names:

• chr4-176893709-G-A
• rs7700025
• ENST00000656694.1:n.384+159C>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000656694.1(ENSG00000287544):​n.384+159C>T variant causes a intron 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: ENSG00000287544 ENST00000656694.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.219
• Publications: 5 publications found

Genes affected

ENSG00000287544 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656694.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287544	ENST00000656694.1		n.384+159C>T		intron	N/A
	LINC02509	ENST00000670563.1		n.351+11281G>A		intron	N/A
	LINC02509	ENST00000769123.1		n.200-14171G>A		intron	N/A

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

African (AFR) AF: 0.388 AC: 16057 AN: 41368

American (AMR) AF: 0.630 AC: 9610 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.722 AC: 2505 AN: 3470

East Asian (EAS) AF: 0.631 AC: 3262 AN: 5168

South Asian (SAS) AF: 0.613 AC: 2950 AN: 4814

European-Finnish (FIN) AF: 0.717 AC: 7575 AN: 10564

Middle Eastern (MID) AF: 0.668 AC: 195 AN: 292

European-Non Finnish (NFE) AF: 0.700 AC: 47557 AN: 67924

Other (OTH) AF: 0.630 AC: 1330 AN: 2112

Alfa AF: 0.661 Hom.: 92561

Bravo AF: 0.588

Asia WGS AF: 0.586 AC: 2040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.66
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs7700025; hg19: chr4-177814863;