rs10737416

Variant summary

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

The XR_949207.2(LOC105373109):​n.63-2274G>T 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 0.339 in 152,078 control chromosomes in the GnomAD database, including 10,594 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 0.34 ( 10594 hom., cov: 32)

Consequence

LOC105373109
XR_949207.2 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.163
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 (EAS) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105373109XR_949207.2 linkuse as main transcriptn.63-2274G>T intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.339
AC:
51577
AN:
151960
Hom.:
10586
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.101
Gnomad AMI
AF:
0.407
Gnomad AMR
AF:
0.434
Gnomad ASJ
AF:
0.366
Gnomad EAS
AF:
0.602
Gnomad SAS
AF:
0.450
Gnomad FIN
AF:
0.422
Gnomad MID
AF:
0.277
Gnomad NFE
AF:
0.421
Gnomad OTH
AF:
0.344
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.339
AC:
51589
AN:
152078
Hom.:
10594
Cov.:
32
AF XY:
0.344
AC XY:
25556
AN XY:
74316
show subpopulations
Gnomad4 AFR
AF:
0.101
Gnomad4 AMR
AF:
0.435
Gnomad4 ASJ
AF:
0.366
Gnomad4 EAS
AF:
0.602
Gnomad4 SAS
AF:
0.450
Gnomad4 FIN
AF:
0.422
Gnomad4 NFE
AF:
0.421
Gnomad4 OTH
AF:
0.345
Alfa
AF:
0.239
Hom.:
629
Bravo
AF:
0.330
Asia WGS
AF:
0.508
AC:
1765
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
4.0
DANN
Benign
0.45

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: rs10737416; hg19: chr1-225074757; API