chr2-175457761-T-C

Variant summary

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

The ENST00000438963.2(ENSG00000229066):​n.782-4904T>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 0.408 in 152,110 control chromosomes in the GnomAD database, including 14,235 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 0.41 ( 14235 hom., cov: 32)

Consequence


ENST00000438963.2 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.760
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=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105373752XR_923596.2 linkuse as main transcriptn.79+3077T>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000438963.2 linkuse as main transcriptn.782-4904T>C intron_variant, non_coding_transcript_variant 3
ENST00000653625.1 linkuse as main transcriptn.947+3077T>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.408
AC:
61948
AN:
151992
Hom.:
14208
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.604
Gnomad AMI
AF:
0.478
Gnomad AMR
AF:
0.442
Gnomad ASJ
AF:
0.359
Gnomad EAS
AF:
0.660
Gnomad SAS
AF:
0.434
Gnomad FIN
AF:
0.220
Gnomad MID
AF:
0.491
Gnomad NFE
AF:
0.290
Gnomad OTH
AF:
0.415
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.408
AC:
62019
AN:
152110
Hom.:
14235
Cov.:
32
AF XY:
0.409
AC XY:
30374
AN XY:
74344
show subpopulations
Gnomad4 AFR
AF:
0.604
Gnomad4 AMR
AF:
0.442
Gnomad4 ASJ
AF:
0.359
Gnomad4 EAS
AF:
0.660
Gnomad4 SAS
AF:
0.433
Gnomad4 FIN
AF:
0.220
Gnomad4 NFE
AF:
0.290
Gnomad4 OTH
AF:
0.415
Alfa
AF:
0.320
Hom.:
18117
Bravo
AF:
0.433
Asia WGS
AF:
0.551
AC:
1916
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
1.1
DANN
Benign
0.28

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: rs2437896; hg19: chr2-176322489; API