chr4-99103732-A-G

Variant summary

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

The NR_037884.1(LOC100507053):​n.428+14448A>G 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 0.338 in 152,092 control chromosomes in the GnomAD database, including 10,342 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 0.34 ( 10342 hom., cov: 32)

Consequence

LOC100507053
NR_037884.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.506
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=-0.97).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LOC100507053NR_037884.1 linkuse as main transcriptn.428+14448A>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENST00000500358.6 linkuse as main transcriptn.428+14448A>G intron_variant, non_coding_transcript_variant 1
ENST00000661393.1 linkuse as main transcriptn.425+14448A>G intron_variant, non_coding_transcript_variant
ENST00000670724.1 linkuse as main transcriptn.480+14448A>G intron_variant, non_coding_transcript_variant
ENST00000691990.1 linkuse as main transcriptn.446+14448A>G intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.338
AC:
51391
AN:
151974
Hom.:
10337
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.134
Gnomad AMI
AF:
0.395
Gnomad AMR
AF:
0.329
Gnomad ASJ
AF:
0.390
Gnomad EAS
AF:
0.129
Gnomad SAS
AF:
0.510
Gnomad FIN
AF:
0.453
Gnomad MID
AF:
0.456
Gnomad NFE
AF:
0.446
Gnomad OTH
AF:
0.350
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.338
AC:
51395
AN:
152092
Hom.:
10342
Cov.:
32
AF XY:
0.341
AC XY:
25359
AN XY:
74356
show subpopulations
Gnomad4 AFR
AF:
0.134
Gnomad4 AMR
AF:
0.329
Gnomad4 ASJ
AF:
0.390
Gnomad4 EAS
AF:
0.129
Gnomad4 SAS
AF:
0.511
Gnomad4 FIN
AF:
0.453
Gnomad4 NFE
AF:
0.446
Gnomad4 OTH
AF:
0.353
Alfa
AF:
0.316
Hom.:
1913
Bravo
AF:
0.313
Asia WGS
AF:
0.374
AC:
1302
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
1.7
DANN
Benign
0.70

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: rs2851275; hg19: chr4-100024883; API