rs7297610

Variant names:

• chr12-69430244-C-T
• rs7297610
• ENST00000776073.1:n.372+6117C>T

Variant summary

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

The ENST00000776073.1(LINC02373):​n.372+6117C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,150 control chromosomes in the GnomAD database, including 2,163 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 0.12 (2163 hom., cov: 32)
• Consequence: LINC02373 ENST00000776073.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231
• Publications: 37 publications found

Genes affected

LINC02373 (HGNC:53295): (long intergenic non-protein coding RNA 2373)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.298 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
LINC02373	ENST00000776073.1	n.372+6117C>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18840 AN: 152032 Hom.: 2161 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.0720

Gnomad ASJ AF: 0.0582

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0218

Gnomad FIN AF: 0.0282

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0631

Gnomad OTH AF: 0.0917

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

GnomAD4 genome AF: 0.124 AC: 18869 AN: 152150 Hom.: 2163 Cov.: 32 AF XY: 0.119 AC XY: 8834 AN XY: 74396

African (AFR) AF: 0.303 AC: 12560 AN: 41462

American (AMR) AF: 0.0719 AC: 1099 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0582 AC: 202 AN: 3468

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5188

South Asian (SAS) AF: 0.0218 AC: 105 AN: 4822

European-Finnish (FIN) AF: 0.0282 AC: 299 AN: 10590

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0631 AC: 4292 AN: 68020

Other (OTH) AF: 0.0908 AC: 191 AN: 2104

Alfa AF: 0.0838 Hom.: 3358

Bravo AF: 0.136

Asia WGS AF: 0.0250 AC: 88 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.0
DANN	Benign	0.59
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs7297610; hg19: chr12-69824024;