rs1900005

chr10-68238298-A-Cchr10-68238298-A-T

Variant summary

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

The ENST00000444086.1(LINC02640):n.61-667T>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 0.598 in 152,038 control chromosomes in the GnomAD database, including 30,618 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 0.60 (30618 hom., cov: 32)
• Consequence: LINC02640 ENST00000444086.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.285

Genes affected

LINC02640 (HGNC:54123): (long intergenic non-protein coding RNA 2640)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02640	XR_001747481.1	n.104-667T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02640	ENST00000444086.1	n.61-667T>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.598 AC: 90873 AN: 151920 Hom.: 30622 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.729

Gnomad NFE AF: 0.757

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.598 AC: 90889 AN: 152038 Hom.: 30618 Cov.: 32 AF XY: 0.596 AC XY: 44300 AN XY: 74314

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.643

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.653

Gnomad4 SAS AF: 0.704

Gnomad4 FIN AF: 0.688

Gnomad4 NFE AF: 0.757

Gnomad4 OTH AF: 0.656

Alfa AF: 0.730 Hom.: 40529

Bravo AF: 0.574

Asia WGS AF: 0.680 AC: 2364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	10
Dann	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1900005; hg19: chr10-69998055;