rs2316640

chr13-55070789-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000616578.1(LINC02335):n.58+7787A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,122 control chromosomes in the GnomAD database, including 3,097 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 0.19 (3097 hom., cov: 32)
• Consequence: LINC02335 ENST00000616578.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31

Genes affected

LINC02335 (HGNC:53255): (long intergenic non-protein coding RNA 2335)

LOC124903234 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903234	XR_007063919.1	n.131+7787A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02335	ENST00000616578.1	n.58+7787A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29408 AN: 152004 Hom.: 3095 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.193 AC: 29435 AN: 152122 Hom.: 3097 Cov.: 32 AF XY: 0.198 AC XY: 14730 AN XY: 74356

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.360

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.192

Alfa AF: 0.200 Hom.: 6492

Bravo AF: 0.187

Asia WGS AF: 0.327 AC: 1137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	4.1
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2316640; hg19: chr13-55644924;