6-35569629-T-C

Variant names:

• chr6-35569629-T-C
• rs3800374
• ENST00000722031.1:n.104-23401T>C

Variant summary

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

The ENST00000722031.1(LINC03135):​n.104-23401T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.823 in 152,146 control chromosomes in the GnomAD database, including 51,632 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 (51632 hom., cov: 33)
• Consequence: LINC03135 ENST00000722031.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 10 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.831 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.104-23401T>C		intron	N/A
	LINC03135	ENST00000722032.1		n.141-23401T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.823 AC: 125133 AN: 152028 Hom.: 51578 Cov.: 33

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.908

Gnomad AMR AF: 0.843

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.822

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.823 AC: 125242 AN: 152146 Hom.: 51632 Cov.: 33 AF XY: 0.823 AC XY: 61198 AN XY: 74396

African (AFR) AF: 0.835 AC: 34630 AN: 41470

American (AMR) AF: 0.843 AC: 12885 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.795 AC: 2756 AN: 3468

East Asian (EAS) AF: 0.801 AC: 4142 AN: 5172

South Asian (SAS) AF: 0.723 AC: 3491 AN: 4830

European-Finnish (FIN) AF: 0.822 AC: 8713 AN: 10602

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.822 AC: 55901 AN: 68002

Other (OTH) AF: 0.794 AC: 1676 AN: 2112

Alfa AF: 0.814 Hom.: 22481

Bravo AF: 0.827

Asia WGS AF: 0.761 AC: 2643 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.68
DANN	Benign	0.78
PhyloP100		-1.3

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: rs3800374;

hg19: chr6-35537406;