chr7-1744899-C-T

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7

The NM_001128636.4(ELFN1):​c.303C>T​(p.Asp101Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00015 in 1,557,566 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00070 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000091 ( 0 hom. )

Consequence

ELFN1
NM_001128636.4 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.70
Variant links:
Genes affected
ELFN1 (HGNC:33154): (extracellular leucine rich repeat and fibronectin type III domain containing 1) Predicted to enable protein phosphatase inhibitor activity. Predicted to be involved in synapse organization. Predicted to be located in dendrite and excitatory synapse. Predicted to be active in extracellular matrix and extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
Variant 7-1744899-C-T is Benign according to our data. Variant chr7-1744899-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 724977.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.7 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ELFN1NM_001128636.4 linkc.303C>T p.Asp101Asp synonymous_variant Exon 4 of 4 ENST00000424383.5 NP_001122108.1 P0C7U0

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ELFN1ENST00000424383.5 linkc.303C>T p.Asp101Asp synonymous_variant Exon 4 of 4 5 NM_001128636.4 ENSP00000456548.1 P0C7U0
ELFN1ENST00000561626.4 linkc.303C>T p.Asp101Asp synonymous_variant Exon 3 of 3 2 ENSP00000457193.1 P0C7U0
ELFN1ENST00000691883.1 linkc.303C>T p.Asp101Asp synonymous_variant Exon 3 of 3 ENSP00000510296.1 P0C7U0

Frequencies

GnomAD3 genomes
AF:
0.000697
AC:
106
AN:
152182
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00200
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00118
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000588
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000182
AC:
30
AN:
164538
Hom.:
0
AF XY:
0.000207
AC XY:
18
AN XY:
86968
show subpopulations
Gnomad AFR exome
AF:
0.00132
Gnomad AMR exome
AF:
0.000557
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000171
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000153
Gnomad OTH exome
AF:
0.000218
GnomAD4 exome
AF:
0.0000911
AC:
128
AN:
1405266
Hom.:
0
Cov.:
31
AF XY:
0.0000836
AC XY:
58
AN XY:
693668
show subpopulations
Gnomad4 AFR exome
AF:
0.00222
Gnomad4 AMR exome
AF:
0.000634
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000137
Gnomad4 SAS exome
AF:
0.0000126
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000157
Gnomad4 OTH exome
AF:
0.000189
GnomAD4 genome
AF:
0.000696
AC:
106
AN:
152300
Hom.:
0
Cov.:
33
AF XY:
0.000752
AC XY:
56
AN XY:
74456
show subpopulations
Gnomad4 AFR
AF:
0.00200
Gnomad4 AMR
AF:
0.00118
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000588
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000458
Hom.:
0
Bravo
AF:
0.000774

ClinVar

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

Submissions by phenotype

not provided Benign:1
May 21, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.56
CADD
Benign
4.7
DANN
Benign
0.85

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs371567558; hg19: chr7-1784535; API