11-65579427-C-G

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001099409.3(EHBP1L1):ā€‹c.249C>Gā€‹(p.Thr83Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000641 in 1,543,936 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā˜…).

Frequency

Genomes: š‘“ 0.00042 ( 0 hom., cov: 30)
Exomes š‘“: 0.00067 ( 2 hom. )

Consequence

EHBP1L1
NM_001099409.3 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.81
Variant links:
Genes affected
EHBP1L1 (HGNC:30682): (EH domain binding protein 1 like 1) Predicted to be involved in actin cytoskeleton organization. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.69).
BP6
Variant 11-65579427-C-G is Benign according to our data. Variant chr11-65579427-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 2641961.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.81 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 2 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
EHBP1L1NM_001099409.3 linkuse as main transcriptc.249C>G p.Thr83Thr synonymous_variant 3/19 ENST00000309295.9 NP_001092879.1 Q8N3D4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
EHBP1L1ENST00000309295.9 linkuse as main transcriptc.249C>G p.Thr83Thr synonymous_variant 3/191 NM_001099409.3 ENSP00000312671.4 Q8N3D4
EHBP1L1ENST00000533237.5 linkuse as main transcriptc.249C>G p.Thr83Thr synonymous_variant 3/125 ENSP00000431996.1 E9PIH6
EHBP1L1ENST00000634639.1 linkuse as main transcriptc.249C>G p.Thr83Thr synonymous_variant 3/125 ENSP00000489002.1 A0A0U1RQH4
EHBP1L1ENST00000531106.1 linkuse as main transcriptn.*47C>G downstream_gene_variant 3

Frequencies

GnomAD3 genomes
AF:
0.000421
AC:
64
AN:
151962
Hom.:
0
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.000169
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000262
Gnomad ASJ
AF:
0.000864
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000706
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000463
AC:
74
AN:
159832
Hom.:
1
AF XY:
0.000624
AC XY:
53
AN XY:
84898
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000212
Gnomad ASJ exome
AF:
0.000906
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000417
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000787
Gnomad OTH exome
AF:
0.000477
GnomAD4 exome
AF:
0.000665
AC:
926
AN:
1391856
Hom.:
2
Cov.:
32
AF XY:
0.000669
AC XY:
459
AN XY:
685640
show subpopulations
Gnomad4 AFR exome
AF:
0.000125
Gnomad4 AMR exome
AF:
0.000257
Gnomad4 ASJ exome
AF:
0.000554
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000367
Gnomad4 FIN exome
AF:
0.000142
Gnomad4 NFE exome
AF:
0.000757
Gnomad4 OTH exome
AF:
0.000606
GnomAD4 genome
AF:
0.000421
AC:
64
AN:
152080
Hom.:
0
Cov.:
30
AF XY:
0.000363
AC XY:
27
AN XY:
74322
show subpopulations
Gnomad4 AFR
AF:
0.000169
Gnomad4 AMR
AF:
0.000262
Gnomad4 ASJ
AF:
0.000864
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000706
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000757
Hom.:
0
Bravo
AF:
0.000638

ClinVar

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

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenJan 01, 2023EHBP1L1: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.69
CADD
Benign
5.5
DANN
Benign
0.61
RBP_binding_hub_radar
0.97
RBP_regulation_power_radar
2.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.070
Details are displayed if max score is > 0.2

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: rs369857321; hg19: chr11-65346898; API