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GeneBe

4-62194862-T-C

Variant summary

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

The ENST00000687436.2(ENSG00000288659):n.374-25469T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.605 in 151,716 control chromosomes in the GnomAD database, including 28,201 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 0.61 ( 28201 hom., cov: 30)

Consequence


ENST00000687436.2 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.243
Variant links:
Genes affected

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=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC101927145XR_938809.3 linkuse as main transcriptn.372-25469T>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000687436.2 linkuse as main transcriptn.374-25469T>C intron_variant, non_coding_transcript_variant
ENST00000676649.1 linkuse as main transcriptn.447-25469T>C intron_variant, non_coding_transcript_variant
ENST00000702460.1 linkuse as main transcriptn.277-19787T>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.605
AC:
91718
AN:
151596
Hom.:
28158
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.697
Gnomad AMI
AF:
0.605
Gnomad AMR
AF:
0.620
Gnomad ASJ
AF:
0.579
Gnomad EAS
AF:
0.585
Gnomad SAS
AF:
0.486
Gnomad FIN
AF:
0.565
Gnomad MID
AF:
0.580
Gnomad NFE
AF:
0.563
Gnomad OTH
AF:
0.615
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.605
AC:
91821
AN:
151716
Hom.:
28201
Cov.:
30
AF XY:
0.603
AC XY:
44662
AN XY:
74126
show subpopulations
Gnomad4 AFR
AF:
0.697
Gnomad4 AMR
AF:
0.620
Gnomad4 ASJ
AF:
0.579
Gnomad4 EAS
AF:
0.585
Gnomad4 SAS
AF:
0.485
Gnomad4 FIN
AF:
0.565
Gnomad4 NFE
AF:
0.563
Gnomad4 OTH
AF:
0.619
Alfa
AF:
0.576
Hom.:
24698
Bravo
AF:
0.615
Asia WGS
AF:
0.581
AC:
2020
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
Cadd
Benign
1.5
Dann
Benign
0.61

Splicing

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: rs4446347; hg19: chr4-63060580; API