chr14-105909907-G-A
Position:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The ENST00000430425.1(IGHD1-7):c.17C>T(p.Ter6=) variant causes a incomplete terminal codon, coding sequence change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000234 in 734,444 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00043 ( 7 hom., cov: 29)
Exomes 𝑓: 0.00019 ( 10 hom. )
Consequence
IGHD1-7
ENST00000430425.1 incomplete_terminal_codon, coding_sequence
ENST00000430425.1 incomplete_terminal_codon, coding_sequence
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.03
Genes affected
IGHD1-7 (HGNC:5486): (immunoglobulin heavy diversity 1-7)
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
Variant 14-105909907-G-A is Benign according to our data. Variant chr14-105909907-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2644928.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 7 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGHD1-7 | ENST00000430425.1 | c.17C>T | p.Ter6= | incomplete_terminal_codon_variant, coding_sequence_variant | 1/1 | P1 | |||
FAM30A | ENST00000693413.1 | n.116-11156G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.000408 AC: 56AN: 137326Hom.: 6 Cov.: 29
GnomAD3 genomes
AF:
AC:
56
AN:
137326
Hom.:
Cov.:
29
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.000189 AC: 113AN: 597084Hom.: 10 Cov.: 0 AF XY: 0.000218 AC XY: 71AN XY: 325514
GnomAD4 exome
AF:
AC:
113
AN:
597084
Hom.:
Cov.:
0
AF XY:
AC XY:
71
AN XY:
325514
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.000430 AC: 59AN: 137360Hom.: 7 Cov.: 29 AF XY: 0.000422 AC XY: 28AN XY: 66326
GnomAD4 genome
AF:
AC:
59
AN:
137360
Hom.:
Cov.:
29
AF XY:
AC XY:
28
AN XY:
66326
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
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 submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2022 | ENSG00000288730: BS2 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at