rs1900005

Variant names:

• chr10-68238298-A-C
• rs1900005
• ENST00000444086.1:n.61-667T>G

Your query was ambiguous. Multiple possible variants found:

• chr10-68238298-A-C
• chr10-68238298-A-T

Variant summary

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

The ENST00000444086.1(LINC02640):​n.61-667T>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.285
• Publications: 14 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000444086.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02640	ENST00000444086.1	TSL:3	n.61-667T>G		intron	N/A

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

African (AFR) AF: 0.267 AC: 11086 AN: 41482

American (AMR) AF: 0.643 AC: 9828 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 2352 AN: 3470

East Asian (EAS) AF: 0.653 AC: 3368 AN: 5156

South Asian (SAS) AF: 0.704 AC: 3392 AN: 4818

European-Finnish (FIN) AF: 0.688 AC: 7266 AN: 10556

Middle Eastern (MID) AF: 0.726 AC: 212 AN: 292

European-Non Finnish (NFE) AF: 0.757 AC: 51467 AN: 67972

Other (OTH) AF: 0.656 AC: 1381 AN: 2104

Alfa AF: 0.732 Hom.: 49849

Bravo AF: 0.574

Asia WGS AF: 0.680 AC: 2364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	10
DANN	Benign	0.90
PhyloP100		0.28

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1900005;

hg19: chr10-69998055;