rs6849561

Variant summary

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

The ENST00000502760.2(ENSG00000291203):​n.772-4794G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 151,902 control chromosomes in the GnomAD database, including 5,471 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 0.27 ( 5469 hom., cov: 32)
Exomes 𝑓: 0.30 ( 2 hom. )

Consequence

ENSG00000291203
ENST00000502760.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.998
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=-0.92).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SEPTIN7P14NR_037630.1 linkuse as main transcriptn.728-4794G>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENSG00000291203ENST00000502760.2 linkuse as main transcriptn.772-4794G>C intron_variant 3
ENSG00000291203ENST00000508519.6 linkuse as main transcriptn.663-106G>C intron_variant 3
ENSG00000291203ENST00000510011.6 linkuse as main transcriptn.661-4794G>C intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.266
AC:
40308
AN:
151732
Hom.:
5464
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.227
Gnomad AMI
AF:
0.280
Gnomad AMR
AF:
0.264
Gnomad ASJ
AF:
0.190
Gnomad EAS
AF:
0.382
Gnomad SAS
AF:
0.177
Gnomad FIN
AF:
0.254
Gnomad MID
AF:
0.206
Gnomad NFE
AF:
0.293
Gnomad OTH
AF:
0.280
GnomAD4 exome
AF:
0.300
AC:
15
AN:
50
Hom.:
2
AF XY:
0.206
AC XY:
7
AN XY:
34
show subpopulations
Gnomad4 EAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.286
Gnomad4 OTH exome
AF:
0.750
GnomAD4 genome
AF:
0.266
AC:
40343
AN:
151852
Hom.:
5469
Cov.:
32
AF XY:
0.264
AC XY:
19565
AN XY:
74216
show subpopulations
Gnomad4 AFR
AF:
0.227
Gnomad4 AMR
AF:
0.264
Gnomad4 ASJ
AF:
0.190
Gnomad4 EAS
AF:
0.383
Gnomad4 SAS
AF:
0.176
Gnomad4 FIN
AF:
0.254
Gnomad4 NFE
AF:
0.293
Gnomad4 OTH
AF:
0.278
Alfa
AF:
0.268
Hom.:
719
Bravo
AF:
0.271
Asia WGS
AF:
0.251
AC:
871
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.23
DANN
Benign
0.67

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: rs6849561; hg19: chr4-120409694; API