21-39800239-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001080444.2(IGSF5):​c.1129-1023C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 152,148 control chromosomes in the GnomAD database, including 6,774 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 0.27 ( 6774 hom., cov: 33)

Consequence

IGSF5
NM_001080444.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.590
Variant links:
Genes affected
IGSF5 (HGNC:5952): (immunoglobulin superfamily member 5) Predicted to enable PDZ domain binding activity. Predicted to be involved in cell-cell adhesion. Predicted to be located in apical plasma membrane. Predicted to be integral component of membrane. Predicted to be active in bicellular tight junction and cell surface. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IGSF5NM_001080444.2 linkuse as main transcriptc.1129-1023C>T intron_variant ENST00000380588.5
IGSF5XM_047440699.1 linkuse as main transcriptc.1399-1023C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IGSF5ENST00000380588.5 linkuse as main transcriptc.1129-1023C>T intron_variant 1 NM_001080444.2 P1
IGSF5ENST00000459922.1 linkuse as main transcriptn.551-1023C>T intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.266
AC:
40386
AN:
152030
Hom.:
6756
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0778
Gnomad AMI
AF:
0.370
Gnomad AMR
AF:
0.433
Gnomad ASJ
AF:
0.375
Gnomad EAS
AF:
0.470
Gnomad SAS
AF:
0.383
Gnomad FIN
AF:
0.307
Gnomad MID
AF:
0.282
Gnomad NFE
AF:
0.305
Gnomad OTH
AF:
0.271
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.266
AC:
40421
AN:
152148
Hom.:
6774
Cov.:
33
AF XY:
0.273
AC XY:
20309
AN XY:
74388
show subpopulations
Gnomad4 AFR
AF:
0.0776
Gnomad4 AMR
AF:
0.434
Gnomad4 ASJ
AF:
0.375
Gnomad4 EAS
AF:
0.471
Gnomad4 SAS
AF:
0.385
Gnomad4 FIN
AF:
0.307
Gnomad4 NFE
AF:
0.305
Gnomad4 OTH
AF:
0.274
Alfa
AF:
0.283
Hom.:
3366
Bravo
AF:
0.269
Asia WGS
AF:
0.392
AC:
1363
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
7.4
DANN
Benign
0.65

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: rs2837227; hg19: chr21-41172166; API