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GeneBe

rs2046210

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The XR_007059816.1(LOC124901435):n.657G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 151844 control chromosomes in the gnomAD Genomes database, including 14105 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.41 ( 14105 hom., cov: 32)

Consequence

LOC124901435
XR_007059816.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Benign criteria provided, single submitter P:1B:1

Conservation

PhyloP100: -0.156

Links

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
?
Variant 6-151627231-G-A is Benign according to our data. Variant chr6-151627231-G-A is described in ClinVar as [Benign]. Clinvar id is 155877.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC124901435XR_007059816.1 linkuse as main transcriptn.657G>A non_coding_transcript_exon_variant 1/2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.407
AC:
61735
AN:
151844
Hom.:
14105
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.621
Gnomad AMI
AF:
0.295
Gnomad AMR
AF:
0.303
Gnomad ASJ
AF:
0.352
Gnomad EAS
AF:
0.348
Gnomad SAS
AF:
0.358
Gnomad FIN
AF:
0.195
Gnomad MID
AF:
0.452
Gnomad NFE
AF:
0.344
Gnomad OTH
AF:
0.420
Alfa
AF:
0.359
Hom.:
13856
Bravo
AF:
0.424
Asia WGS
AF:
0.380
AC:
1322
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Pathogenic:1Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Estrogen resistance syndrome Pathogenic:1
Likely pathogenic, no assertion criteria providedresearchDepartment of Breast and Endocrine Surgery, Kumamoto UniversityMar 01, 2014- -
not specified Benign:1
Benign, criteria provided, single submitterresearchH3Africa ConsortiumOct 28, 2020While the frequency of the alternate allele in gnoMAD v2.0.2 is 0.729, its frequency in African populations is >5%. This suggests that previous classifications of this variant as pathogenic are in error. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
Cadd
Benign
0.43
Dann
Benign
0.39

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: rs2046210; hg19: chr6-151948366; COSMIC: COSV53317094; API