rs7443800

Variant summary

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

The XR_001743014.1(LOC107986487):​n.90+696C>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 0.324 in 151,332 control chromosomes in the GnomAD database, including 9,276 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 0.32 ( 9276 hom., cov: 29)

Consequence

LOC107986487
XR_001743014.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.143
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=-0.8).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LOC107986487XR_001743014.1 linkuse as main transcriptn.90+696C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENST00000697530.1 linkuse as main transcriptn.1220-4325G>A intron_variant, non_coding_transcript_variant
ENST00000697531.1 linkuse as main transcriptn.655-4325G>A intron_variant, non_coding_transcript_variant
ENST00000697534.1 linkuse as main transcriptn.622-4325G>A intron_variant, non_coding_transcript_variant
ENST00000697538.1 linkuse as main transcriptn.321-4325G>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.324
AC:
49035
AN:
151210
Hom.:
9275
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.125
Gnomad AMI
AF:
0.478
Gnomad AMR
AF:
0.315
Gnomad ASJ
AF:
0.383
Gnomad EAS
AF:
0.338
Gnomad SAS
AF:
0.295
Gnomad FIN
AF:
0.457
Gnomad MID
AF:
0.360
Gnomad NFE
AF:
0.422
Gnomad OTH
AF:
0.340
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.324
AC:
49047
AN:
151332
Hom.:
9276
Cov.:
29
AF XY:
0.324
AC XY:
23936
AN XY:
73946
show subpopulations
Gnomad4 AFR
AF:
0.125
Gnomad4 AMR
AF:
0.314
Gnomad4 ASJ
AF:
0.383
Gnomad4 EAS
AF:
0.338
Gnomad4 SAS
AF:
0.296
Gnomad4 FIN
AF:
0.457
Gnomad4 NFE
AF:
0.422
Gnomad4 OTH
AF:
0.338
Alfa
AF:
0.386
Hom.:
8040
Bravo
AF:
0.306
Asia WGS
AF:
0.307
AC:
1067
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
6.9
DANN
Benign
0.56

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: rs7443800; hg19: chr5-175559839; API