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GeneBe

rs2965306

Positions:

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4BA1

The ENST00000662551.1(ENSG00000259754):​n.189-72971A>G variant causes a intron, non coding transcript change. The variant allele was found at a frequency of 0.658 in 152,002 control chromosomes in the GnomAD database, including 38,176 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 0.66 ( 38176 hom., cov: 32)

Consequence


ENST00000662551.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.07
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.18).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC124900354XR_001751516.3 linkuse as main transcriptn.142+35234A>G intron_variant, non_coding_transcript_variant
LOC124900354XR_001751517.2 linkuse as main transcriptn.142+35234A>G intron_variant, non_coding_transcript_variant
LOC124900354XR_001751518.3 linkuse as main transcriptn.82+4376A>G intron_variant, non_coding_transcript_variant
LOC124900354XR_007064618.1 linkuse as main transcriptn.143-29618A>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000662551.1 linkuse as main transcriptn.189-72971A>G intron_variant, non_coding_transcript_variant
ENST00000560900.1 linkuse as main transcriptn.195+35234A>G intron_variant, non_coding_transcript_variant 4
ENST00000664705.1 linkuse as main transcriptn.189-72971A>G intron_variant, non_coding_transcript_variant
ENST00000665188.1 linkuse as main transcriptn.69-72971A>G intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.658
AC:
99985
AN:
151882
Hom.:
38172
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.282
Gnomad AMI
AF:
0.900
Gnomad AMR
AF:
0.629
Gnomad ASJ
AF:
0.908
Gnomad EAS
AF:
0.359
Gnomad SAS
AF:
0.719
Gnomad FIN
AF:
0.842
Gnomad MID
AF:
0.886
Gnomad NFE
AF:
0.864
Gnomad OTH
AF:
0.708
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.658
AC:
100020
AN:
152002
Hom.:
38176
Cov.:
32
AF XY:
0.658
AC XY:
48894
AN XY:
74322
show subpopulations
Gnomad4 AFR
AF:
0.283
Gnomad4 AMR
AF:
0.629
Gnomad4 ASJ
AF:
0.908
Gnomad4 EAS
AF:
0.359
Gnomad4 SAS
AF:
0.720
Gnomad4 FIN
AF:
0.842
Gnomad4 NFE
AF:
0.864
Gnomad4 OTH
AF:
0.705
Alfa
AF:
0.832
Hom.:
66802
Bravo
AF:
0.622
Asia WGS
AF:
0.517
AC:
1789
AN:
3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.18
CADD
Benign
19
DANN
Benign
0.88

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: rs2965306; hg19: chr15-48211935; API