rs10498640

Variant names:

• chr14-94960513-G-A
• rs10498640
• ENST00000553435.1:n.526-25C>T

Variant summary

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

The ENST00000553435.1(LINC02279):​n.526-25C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.022 in 152,240 control chromosomes in the GnomAD database, including 60 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 0.022 (60 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINC02279 ENST00000553435.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261
• Publications: 1 publications found

Genes affected

LINC02279 (HGNC:53195): (long intergenic non-protein coding RNA 2279)

LOC124903370 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.0789 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903370	XR_007064318.1	n.258-25C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02279	ENST00000553435.1	n.526-25C>T		intron_variant	Intron 4 of 4	5
LINC02279	ENST00000840070.1	n.297-25C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0220 AC: 3341 AN: 152122 Hom.: 60 Cov.: 32

Gnomad AFR AF: 0.0330

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0119

Gnomad ASJ AF: 0.0423

Gnomad EAS AF: 0.0855

Gnomad SAS AF: 0.0299

Gnomad FIN AF: 0.0126

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0130

Gnomad OTH AF: 0.0172

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0220 AC: 3349 AN: 152240 Hom.: 60 Cov.: 32 AF XY: 0.0216 AC XY: 1610 AN XY: 74440

African (AFR) AF: 0.0331 AC: 1373 AN: 41536

American (AMR) AF: 0.0119 AC: 182 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0423 AC: 147 AN: 3472

East Asian (EAS) AF: 0.0855 AC: 443 AN: 5180

South Asian (SAS) AF: 0.0299 AC: 144 AN: 4814

European-Finnish (FIN) AF: 0.0126 AC: 134 AN: 10598

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0130 AC: 885 AN: 68032

Other (OTH) AF: 0.0180 AC: 38 AN: 2114

Alfa AF: 0.0171 Hom.: 5

Bravo AF: 0.0226

Asia WGS AF: 0.0490 AC: 169 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	4.6
DANN	Benign	0.86
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs10498640; hg19: chr14-95426850;