rs7246657

Variant names:

• chr19-37256206-T-C
• rs7246657
• ENST00000592712.5:n.342-193T>C

Variant summary

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

The ENST00000666743.1(LINC01535):​n.172T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 152,104 control chromosomes in the GnomAD database, including 7,055 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 0.27 (7055 hom., cov: 32)
• Consequence: LINC01535 ENST00000666743.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 19 publications found

Genes affected

LINC01535 (HGNC:51282): (long intergenic non-protein coding RNA 1535)

ENSG00000267605 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.13).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000666743.1. 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
	LINC01535	NR_110718.1		n.383-193T>C		intron	N/A
	LINC01535	NR_110719.1		n.382+224T>C		intron	N/A
	LINC01535	NR_110720.2		n.356+224T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01535	ENST00000592712.5	TSL:1	n.342-193T>C		intron	N/A
	LINC01535	ENST00000666743.1		n.172T>C		non_coding_transcript_exon	Exon 3 of 7
	LINC01535	ENST00000692449.1		n.383T>C		non_coding_transcript_exon	Exon 3 of 8

Frequencies

GnomAD3 genomes AF: 0.270 AC: 41057 AN: 151986 Hom.: 7044 Cov.: 32

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.270 AC: 41097 AN: 152104 Hom.: 7055 Cov.: 32 AF XY: 0.272 AC XY: 20205 AN XY: 74362

African (AFR) AF: 0.475 AC: 19671 AN: 41408

American (AMR) AF: 0.271 AC: 4139 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 802 AN: 3468

East Asian (EAS) AF: 0.307 AC: 1593 AN: 5182

South Asian (SAS) AF: 0.350 AC: 1687 AN: 4826

European-Finnish (FIN) AF: 0.168 AC: 1777 AN: 10598

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10571 AN: 68010

Other (OTH) AF: 0.268 AC: 567 AN: 2112

Alfa AF: 0.186 Hom.: 3149

Bravo AF: 0.284

Asia WGS AF: 0.345 AC: 1201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.15
DANN	Benign	0.25
PhyloP100		-1.7

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: rs7246657;

hg19: chr19-37747108;