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GeneBe

rs10499194

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000635999.1(LINC03004):n.433+7376C>T 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 0.238 in 151332 control chromosomes in the gnomAD Genomes database, including 4586 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 0.24 ( 4586 hom., cov: 29)

Consequence

LINC03004
ENST00000635999.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.426

Links

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
?
GnomAd highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LINC03004ENST00000635999.1 linkuse as main transcriptn.433+7376C>T intron_variant, non_coding_transcript_variant 5
LINC03004ENST00000638039.1 linkuse as main transcriptn.439-5594C>T intron_variant, non_coding_transcript_variant 5
LINC03004ENST00000646621.1 linkuse as main transcriptn.415-5594C>T intron_variant, non_coding_transcript_variant
LINC03004ENST00000666119.1 linkuse as main transcriptn.393-5594C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.238
AC:
35944
AN:
151332
Hom.:
4586
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.172
Gnomad AMI
AF:
0.401
Gnomad AMR
AF:
0.287
Gnomad ASJ
AF:
0.356
Gnomad EAS
AF:
0.0392
Gnomad SAS
AF:
0.257
Gnomad FIN
AF:
0.224
Gnomad MID
AF:
0.297
Gnomad NFE
AF:
0.274
Gnomad OTH
AF:
0.240
Alfa
AF:
0.259
Hom.:
530
Bravo
AF:
0.242
Asia WGS
AF:
0.148
AC:
517
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
Cadd
Benign
5.2
Dann
Benign
0.65

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10499194; hg19: chr6-138002637; API