rs5030344
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_000201.3(ICAM1):c.67+1751G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00758 in 152,262 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0076 ( 9 hom., cov: 30)
Consequence
ICAM1
NM_000201.3 intron
NM_000201.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0230
Genes affected
ICAM1 (HGNC:5344): (intercellular adhesion molecule 1) This gene encodes a cell surface glycoprotein which is typically expressed on endothelial cells and cells of the immune system. It binds to integrins of type CD11a / CD18, or CD11b / CD18 and is also exploited by Rhinovirus as a receptor. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00758 (1154/152262) while in subpopulation AFR AF= 0.0261 (1086/41544). AF 95% confidence interval is 0.0248. There are 9 homozygotes in gnomad4. There are 549 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 9 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ICAM1 | NM_000201.3 | c.67+1751G>A | intron_variant | ENST00000264832.8 | |||
LIMASI | XR_007067138.1 | n.131-6183C>T | intron_variant, non_coding_transcript_variant | ||||
LIMASI | XR_007067137.1 | n.131-6183C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ICAM1 | ENST00000264832.8 | c.67+1751G>A | intron_variant | 1 | NM_000201.3 | P1 | |||
LIMASI | ENST00000592893.1 | n.141+11991C>T | intron_variant, non_coding_transcript_variant | 3 | |||||
ICAM1 | ENST00000423829.2 | c.67+1751G>A | intron_variant | 2 | |||||
ICAM1 | ENST00000588645.1 | c.67+1751G>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00757 AC: 1152AN: 152144Hom.: 9 Cov.: 30
GnomAD3 genomes
?
AF:
AC:
1152
AN:
152144
Hom.:
Cov.:
30
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.00758 AC: 1154AN: 152262Hom.: 9 Cov.: 30 AF XY: 0.00738 AC XY: 549AN XY: 74440
GnomAD4 genome
?
AF:
AC:
1154
AN:
152262
Hom.:
Cov.:
30
AF XY:
AC XY:
549
AN XY:
74440
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.:
Bravo
AF:
Asia WGS
AF:
AC:
4
AN:
3478
ClinVar
Not reported inComputational 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