chr4-137206691-T-G

Variant names:

• chr4-137206691-T-G
• rs17644158
• ENST00000505736.5:n.63+6046A>C

Variant summary

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

The ENST00000505736.5(LINC02511):​n.63+6046A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 151,866 control chromosomes in the GnomAD database, including 1,973 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 0.16 (1973 hom., cov: 32)
• Consequence: LINC02511 ENST00000505736.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.694
• Publications: 3 publications found

Genes affected

LINC02511 (HGNC:53500): (long intergenic non-protein coding RNA 2511)

LINC02510 (HGNC:53499): (long intergenic non-protein coding RNA 2510)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02511	NR_149105.1	n.63+6046A>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02511	ENST00000505736.5	n.63+6046A>C		intron_variant	Intron 1 of 3	5
LINC02511	ENST00000652184.1	n.54+6046A>C		intron_variant	Intron 1 of 5
LINC02511	ENST00000656187.1	n.52+6046A>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23613 AN: 151748 Hom.: 1975 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.0516

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.155 AC: 23611 AN: 151866 Hom.: 1973 Cov.: 32 AF XY: 0.157 AC XY: 11628 AN XY: 74234

African (AFR) AF: 0.126 AC: 5237 AN: 41464

American (AMR) AF: 0.145 AC: 2198 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1107 AN: 3462

East Asian (EAS) AF: 0.209 AC: 1079 AN: 5158

South Asian (SAS) AF: 0.241 AC: 1162 AN: 4818

European-Finnish (FIN) AF: 0.124 AC: 1309 AN: 10594

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11004 AN: 67862

Other (OTH) AF: 0.170 AC: 358 AN: 2104

Alfa AF: 0.0898 Hom.: 160

Bravo AF: 0.154

Asia WGS AF: 0.161 AC: 558 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.56
DANN	Benign	0.75
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs17644158; hg19: chr4-138127845;