rs2660753

Variant names:

• chr3-87061524-T-C
• rs2660753
• ENST00000774840.1:n.508+19817T>C

Variant summary

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

The ENST00000774840.1(LINC00506):​n.508+19817T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 152,054 control chromosomes in the GnomAD database, including 46,501 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 0.76 (46501 hom., cov: 31)
• Consequence: LINC00506 ENST00000774840.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15
• Publications: 143 publications found

Genes affected

LINC00506 (HGNC:43557): (long intergenic non-protein coding RNA 506)

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 (NFE) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00506	ENST00000774840.1	n.508+19817T>C		intron_variant	Intron 3 of 3
LINC00506	ENST00000774841.1	n.454+19817T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.761 AC: 115690 AN: 151936 Hom.: 46491 Cov.: 31

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.889

Gnomad AMR AF: 0.825

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.926

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.888

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.761 AC: 115728 AN: 152054 Hom.: 46501 Cov.: 31 AF XY: 0.762 AC XY: 56658 AN XY: 74324

African (AFR) AF: 0.485 AC: 20095 AN: 41420

American (AMR) AF: 0.825 AC: 12604 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.779 AC: 2702 AN: 3470

East Asian (EAS) AF: 0.743 AC: 3839 AN: 5170

South Asian (SAS) AF: 0.763 AC: 3678 AN: 4818

European-Finnish (FIN) AF: 0.926 AC: 9822 AN: 10606

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.888 AC: 60330 AN: 67974

Other (OTH) AF: 0.777 AC: 1637 AN: 2106

Alfa AF: 0.840 Hom.: 199642

Bravo AF: 0.741

Asia WGS AF: 0.717 AC: 2494 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.2
DANN	Benign	0.37
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs2660753; hg19: chr3-87110674;