3-34497020-T-C

Variant names:

• chr3-34497020-T-C
• rs1919624
• ENST00000424786.5:n.571-59568T>C

Variant summary

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

The ENST00000424786.5(LINC01811):​n.571-59568T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 152,104 control chromosomes in the GnomAD database, including 11,148 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 0.38 (11148 hom., cov: 33)
• Consequence: LINC01811 ENST00000424786.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220
• Publications: 1 publications found

Genes affected

LINC01811 (HGNC:52615): (long intergenic non-protein coding RNA 1811)

LOC124909364 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124909364	XR_007095864.1	n.6057-152T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01811	ENST00000424786.5	n.571-59568T>C		intron_variant	Intron 6 of 7	5
LINC01811	ENST00000655650.1	n.310-54387T>C		intron_variant	Intron 3 of 6
LINC01811	ENST00000656055.1	n.542-54382T>C		intron_variant	Intron 5 of 9

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57682 AN: 151986 Hom.: 11144 Cov.: 33

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.380 AC: 57727 AN: 152104 Hom.: 11148 Cov.: 33 AF XY: 0.385 AC XY: 28630 AN XY: 74338

African (AFR) AF: 0.338 AC: 14042 AN: 41488

American (AMR) AF: 0.463 AC: 7075 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1223 AN: 3472

East Asian (EAS) AF: 0.518 AC: 2678 AN: 5168

South Asian (SAS) AF: 0.530 AC: 2553 AN: 4818

European-Finnish (FIN) AF: 0.384 AC: 4059 AN: 10566

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.366 AC: 24901 AN: 68002

Other (OTH) AF: 0.390 AC: 824 AN: 2114

Alfa AF: 0.361 Hom.: 5072

Bravo AF: 0.383

Asia WGS AF: 0.485 AC: 1685 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.64
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs1919624; hg19: chr3-34538512;