chr6-130869620-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001431.4(EPB41L2):c.2550C>T(p.Asn850=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00155 in 1,614,108 control chromosomes in the GnomAD database, including 41 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0082 ( 27 hom., cov: 32)
Exomes 𝑓: 0.00085 ( 14 hom. )
Consequence
EPB41L2
NM_001431.4 synonymous
NM_001431.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.41
Genes affected
EPB41L2 (HGNC:3379): (erythrocyte membrane protein band 4.1 like 2) Predicted to enable PH domain binding activity; cytoskeletal protein binding activity; and structural molecule activity. Involved in positive regulation of protein localization to cell cortex. Located in cell junction; nucleoplasm; and plasma membrane. Colocalizes with COP9 signalosome. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
?
Variant 6-130869620-G-A is Benign according to our data. Variant chr6-130869620-G-A is described in ClinVar as [Benign]. Clinvar id is 785179.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.41 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00824 (1255/152226) while in subpopulation AFR AF= 0.0292 (1211/41528). AF 95% confidence interval is 0.0278. There are 27 homozygotes in gnomad4. There are 600 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 25 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPB41L2 | NM_001431.4 | c.2550C>T | p.Asn850= | synonymous_variant | 15/20 | ENST00000337057.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPB41L2 | ENST00000337057.8 | c.2550C>T | p.Asn850= | synonymous_variant | 15/20 | 1 | NM_001431.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00811 AC: 1233AN: 152108Hom.: 25 Cov.: 32
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GnomAD3 exomes AF: 0.00226 AC: 569AN: 251402Hom.: 5 AF XY: 0.00175 AC XY: 238AN XY: 135866
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GnomAD4 exome AF: 0.000848 AC: 1239AN: 1461882Hom.: 14 Cov.: 31 AF XY: 0.000736 AC XY: 535AN XY: 727240
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GnomAD4 genome ? AF: 0.00824 AC: 1255AN: 152226Hom.: 27 Cov.: 32 AF XY: 0.00806 AC XY: 600AN XY: 74434
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 09, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at