chr6-95928967-C-T

Variant summary

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

The ENST00000658251.1(ENSG00000287578):​n.76-4817G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 151,982 control chromosomes in the GnomAD database, including 7,510 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 0.28 ( 7510 hom., cov: 31)

Consequence

ENSG00000287578
ENST00000658251.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.787
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 (NFE) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC107986626XR_001744263.2 linkn.148-4817G>A intron_variant Intron 1 of 2
LOC107986626XR_001744264.2 linkn.148-4817G>A intron_variant Intron 1 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000287578ENST00000658251.1 linkn.76-4817G>A intron_variant Intron 1 of 2
ENSG00000287578ENST00000668456.1 linkn.106-4817G>A intron_variant Intron 1 of 2

Frequencies

GnomAD3 genomes
AF:
0.284
AC:
43201
AN:
151864
Hom.:
7510
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.101
Gnomad AMI
AF:
0.358
Gnomad AMR
AF:
0.271
Gnomad ASJ
AF:
0.367
Gnomad EAS
AF:
0.105
Gnomad SAS
AF:
0.235
Gnomad FIN
AF:
0.347
Gnomad MID
AF:
0.386
Gnomad NFE
AF:
0.400
Gnomad OTH
AF:
0.316
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.284
AC:
43195
AN:
151982
Hom.:
7510
Cov.:
31
AF XY:
0.279
AC XY:
20700
AN XY:
74256
show subpopulations
Gnomad4 AFR
AF:
0.101
Gnomad4 AMR
AF:
0.271
Gnomad4 ASJ
AF:
0.367
Gnomad4 EAS
AF:
0.106
Gnomad4 SAS
AF:
0.235
Gnomad4 FIN
AF:
0.347
Gnomad4 NFE
AF:
0.400
Gnomad4 OTH
AF:
0.314
Alfa
AF:
0.367
Hom.:
4726
Bravo
AF:
0.271
Asia WGS
AF:
0.181
AC:
629
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
6.9
DANN
Benign
0.69

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: rs6925466; hg19: chr6-96376843; COSMIC: COSV60251866; API