XR_001747481.1:n.36+298A>T

Variant names:

• chr10-68243826-T-A
• rs7896916
• XR_001747481.1:n.36+298A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The XR_001747481.1(LINC02640):​n.36+298A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0225 in 152,070 control chromosomes in the GnomAD database, including 56 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 0.023 (56 hom., cov: 31)
• Consequence: LINC02640 XR_001747481.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223
• Publications: 4 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=-0.89).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0225 (3426/152070) while in subpopulation SAS AF = 0.0352 (169/4802). AF 95% confidence interval is 0.0328. There are 56 homozygotes in GnomAd4. There are 1627 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 56 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02640	XR_001747481.1	n.36+298A>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0225 AC: 3423 AN: 151952 Hom.: 55 Cov.: 31

Gnomad AFR AF: 0.00593

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0189

Gnomad ASJ AF: 0.0254

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0343

Gnomad FIN AF: 0.0199

Gnomad MID AF: 0.0255

Gnomad NFE AF: 0.0339

Gnomad OTH AF: 0.0278

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

GnomAD4 genome AF: 0.0225 AC: 3426 AN: 152070 Hom.: 56 Cov.: 31 AF XY: 0.0219 AC XY: 1627 AN XY: 74336

African (AFR) AF: 0.00591 AC: 245 AN: 41426

American (AMR) AF: 0.0189 AC: 288 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0254 AC: 88 AN: 3468

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5160

South Asian (SAS) AF: 0.0352 AC: 169 AN: 4802

European-Finnish (FIN) AF: 0.0199 AC: 211 AN: 10608

Middle Eastern (MID) AF: 0.0205 AC: 6 AN: 292

European-Non Finnish (NFE) AF: 0.0340 AC: 2310 AN: 68014

Other (OTH) AF: 0.0275 AC: 58 AN: 2112

Alfa AF: 0.0287 Hom.: 12

Bravo AF: 0.0213

Asia WGS AF: 0.0130 AC: 45 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.67
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs7896916; hg19: chr10-70003583;