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GeneBe

rs6887695

Variant summary

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

The ENST00000635333.1(null):n.327+3060G>C 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 0.346 in 151,962 control chromosomes in the GnomAD database, including 9,329 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 0.35 ( 9329 hom., cov: 32)

Consequence


ENST00000635333.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0940
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.413 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
ENST00000635333.1 linkuse as main transcriptn.327+3060G>C intron_variant, non_coding_transcript_variant 5
ENST00000641150.1 linkuse as main transcriptn.533-20887G>C intron_variant, non_coding_transcript_variant
ENST00000648969.1 linkuse as main transcriptn.54-20887G>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.346
AC:
52573
AN:
151844
Hom.:
9315
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.407
Gnomad AMI
AF:
0.301
Gnomad AMR
AF:
0.340
Gnomad ASJ
AF:
0.287
Gnomad EAS
AF:
0.427
Gnomad SAS
AF:
0.365
Gnomad FIN
AF:
0.297
Gnomad MID
AF:
0.376
Gnomad NFE
AF:
0.314
Gnomad OTH
AF:
0.357
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.346
AC:
52621
AN:
151962
Hom.:
9329
Cov.:
32
AF XY:
0.346
AC XY:
25693
AN XY:
74262
show subpopulations
Gnomad4 AFR
AF:
0.407
Gnomad4 AMR
AF:
0.341
Gnomad4 ASJ
AF:
0.287
Gnomad4 EAS
AF:
0.428
Gnomad4 SAS
AF:
0.365
Gnomad4 FIN
AF:
0.297
Gnomad4 NFE
AF:
0.314
Gnomad4 OTH
AF:
0.359
Alfa
AF:
0.322
Hom.:
4297
Bravo
AF:
0.353
Asia WGS
AF:
0.440
AC:
1530
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
Cadd
Benign
2.4
Dann
Benign
0.63

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: rs6887695; hg19: chr5-158822645; API