rs763110

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The variant allele was found at a frequency of 0.488 in 151,968 control chromosomes in the GnomAD database, including 21,522 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.49 ( 21522 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.80
Variant links:

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ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
Variant 1-172658358-C-T is Benign according to our data. Variant chr1-172658358-C-T is described in ClinVar as [Benign]. Clinvar id is 1165021.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.488
AC:
74089
AN:
151850
Hom.:
21468
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.810
Gnomad AMI
AF:
0.443
Gnomad AMR
AF:
0.397
Gnomad ASJ
AF:
0.467
Gnomad EAS
AF:
0.273
Gnomad SAS
AF:
0.579
Gnomad FIN
AF:
0.252
Gnomad MID
AF:
0.500
Gnomad NFE
AF:
0.361
Gnomad OTH
AF:
0.481
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.488
AC:
74198
AN:
151968
Hom.:
21522
Cov.:
32
AF XY:
0.483
AC XY:
35845
AN XY:
74270
show subpopulations
Gnomad4 AFR
AF:
0.810
Gnomad4 AMR
AF:
0.396
Gnomad4 ASJ
AF:
0.467
Gnomad4 EAS
AF:
0.272
Gnomad4 SAS
AF:
0.581
Gnomad4 FIN
AF:
0.252
Gnomad4 NFE
AF:
0.361
Gnomad4 OTH
AF:
0.489
Alfa
AF:
0.398
Hom.:
14481
Bravo
AF:
0.507
Asia WGS
AF:
0.477
AC:
1660
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Autoimmune lymphoproliferative syndrome type 1 Benign:1
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 19, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.10
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: rs763110; hg19: chr1-172627498; COSMIC: COSV60680908; API