rs7969759

Variant summary

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

The XR_001749186.2(LOC105369812):​n.1912+9880G>A 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 0.0706 in 152,200 control chromosomes in the GnomAD database, including 879 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 0.071 ( 879 hom., cov: 32)

Consequence

LOC105369812
XR_001749186.2 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00700
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=-0.94).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105369812XR_001749186.2 linkuse as main transcriptn.1912+9880G>A intron_variant, non_coding_transcript_variant
LOC105369812XR_945043.3 linkuse as main transcriptn.1912+9880G>A intron_variant, non_coding_transcript_variant
LOC124903072XR_007063567.1 linkuse as main transcript upstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.0705
AC:
10722
AN:
152082
Hom.:
875
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.172
Gnomad AMI
AF:
0.0230
Gnomad AMR
AF:
0.122
Gnomad ASJ
AF:
0.00548
Gnomad EAS
AF:
0.223
Gnomad SAS
AF:
0.0358
Gnomad FIN
AF:
0.00867
Gnomad MID
AF:
0.0316
Gnomad NFE
AF:
0.00204
Gnomad OTH
AF:
0.0712
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0706
AC:
10744
AN:
152200
Hom.:
879
Cov.:
32
AF XY:
0.0728
AC XY:
5414
AN XY:
74410
show subpopulations
Gnomad4 AFR
AF:
0.171
Gnomad4 AMR
AF:
0.123
Gnomad4 ASJ
AF:
0.00548
Gnomad4 EAS
AF:
0.223
Gnomad4 SAS
AF:
0.0361
Gnomad4 FIN
AF:
0.00867
Gnomad4 NFE
AF:
0.00203
Gnomad4 OTH
AF:
0.0705
Alfa
AF:
0.0284
Hom.:
345
Bravo
AF:
0.0873
Asia WGS
AF:
0.114
AC:
395
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
2.3
DANN
Benign
0.25

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: rs7969759; hg19: chr12-67829703; API