2-76267835-T-C

Variant summary

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

The ENST00000654219.1(ENSG00000287172):​n.84-73718T>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 0.957 in 151,600 control chromosomes in the GnomAD database, including 69,445 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 0.96 ( 69445 hom., cov: 27)

Consequence


ENST00000654219.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.168
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=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.969 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENST00000654219.1 linkuse as main transcriptn.84-73718T>C intron_variant, non_coding_transcript_variant
ENST00000668214.1 linkuse as main transcriptn.56-73718T>C intron_variant, non_coding_transcript_variant
ENST00000669228.1 linkuse as main transcriptn.84-73718T>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.957
AC:
144967
AN:
151484
Hom.:
69402
Cov.:
27
show subpopulations
Gnomad AFR
AF:
0.935
Gnomad AMI
AF:
0.944
Gnomad AMR
AF:
0.979
Gnomad ASJ
AF:
0.984
Gnomad EAS
AF:
0.992
Gnomad SAS
AF:
0.978
Gnomad FIN
AF:
0.935
Gnomad MID
AF:
0.991
Gnomad NFE
AF:
0.963
Gnomad OTH
AF:
0.967
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.957
AC:
145068
AN:
151600
Hom.:
69445
Cov.:
27
AF XY:
0.957
AC XY:
70844
AN XY:
74040
show subpopulations
Gnomad4 AFR
AF:
0.935
Gnomad4 AMR
AF:
0.979
Gnomad4 ASJ
AF:
0.984
Gnomad4 EAS
AF:
0.992
Gnomad4 SAS
AF:
0.978
Gnomad4 FIN
AF:
0.935
Gnomad4 NFE
AF:
0.963
Gnomad4 OTH
AF:
0.968
Alfa
AF:
0.962
Hom.:
7858
Bravo
AF:
0.960
Asia WGS
AF:
0.978
AC:
3401
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
5.4
DANN
Benign
0.44

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: rs1526651; hg19: chr2-76494961; API