rs4713897

Variant names:

• chr6-35560793-A-G
• rs4713897
• ENST00000722031.1:n.103+15860A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-35560793-A-G
• chr6-35560793-A-T

Variant summary

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

The ENST00000722031.1(LINC03135):​n.103+15860A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.824 in 151,694 control chromosomes in the GnomAD database, including 51,648 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 0.82 (51648 hom., cov: 29)
• Consequence: LINC03135 ENST00000722031.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.616
• Publications: 5 publications found

Genes affected

LINC03135 (HGNC:58100):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000722031.1. 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
	LINC03135	ENST00000722031.1		n.103+15860A>G		intron	N/A
	LINC03135	ENST00000722032.1		n.140+15860A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.824 AC: 124955 AN: 151576 Hom.: 51592 Cov.: 29

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.920

Gnomad AMR AF: 0.846

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.842

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.824 AC: 125071 AN: 151694 Hom.: 51648 Cov.: 29 AF XY: 0.825 AC XY: 61166 AN XY: 74138

African (AFR) AF: 0.837 AC: 34525 AN: 41252

American (AMR) AF: 0.846 AC: 12891 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.786 AC: 2727 AN: 3470

East Asian (EAS) AF: 0.854 AC: 4415 AN: 5168

South Asian (SAS) AF: 0.733 AC: 3530 AN: 4814

European-Finnish (FIN) AF: 0.842 AC: 8855 AN: 10520

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.815 AC: 55391 AN: 67932

Other (OTH) AF: 0.801 AC: 1683 AN: 2102

Alfa AF: 0.819 Hom.: 60425

Bravo AF: 0.827

Asia WGS AF: 0.809 AC: 2811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.24
DANN	Benign	0.57
PhyloP100		-0.62

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4713897;

hg19: chr6-35528570;