rs10167992

Positions:

Variant summary

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

The ENST00000356150.10(SH3YL1):​c.1+714A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.913 in 154,280 control chromosomes in the GnomAD database, including 64,421 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 0.91 ( 63580 hom., cov: 33)
Exomes 𝑓: 0.90 ( 841 hom. )

Consequence

SH3YL1
ENST00000356150.10 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.906
Variant links:
Genes affected
SH3YL1 (HGNC:29546): (SH3 and SYLF domain containing 1) Enables phosphatase binding activity and phosphatidylinositol binding activity. Predicted to act upstream of or within phosphatidylinositol biosynthetic process and regulation of ruffle assembly. Located in ruffle membrane. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.96 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SH3YL1NM_015677.4 linkuse as main transcriptc.1+714A>G intron_variant ENST00000356150.10 NP_056492.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SH3YL1ENST00000356150.10 linkuse as main transcriptc.1+714A>G intron_variant 1 NM_015677.4 ENSP00000348471 P1Q96HL8-1

Frequencies

GnomAD3 genomes
AF:
0.913
AC:
138888
AN:
152104
Hom.:
63528
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.968
Gnomad AMI
AF:
0.826
Gnomad AMR
AF:
0.893
Gnomad ASJ
AF:
0.885
Gnomad EAS
AF:
0.891
Gnomad SAS
AF:
0.921
Gnomad FIN
AF:
0.843
Gnomad MID
AF:
0.908
Gnomad NFE
AF:
0.899
Gnomad OTH
AF:
0.907
GnomAD4 exome
AF:
0.905
AC:
1862
AN:
2058
Hom.:
841
Cov.:
0
AF XY:
0.901
AC XY:
1033
AN XY:
1146
show subpopulations
Gnomad4 AFR exome
AF:
0.900
Gnomad4 AMR exome
AF:
0.902
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.850
Gnomad4 SAS exome
AF:
0.930
Gnomad4 FIN exome
AF:
0.800
Gnomad4 NFE exome
AF:
0.907
Gnomad4 OTH exome
AF:
0.931
GnomAD4 genome
AF:
0.913
AC:
138997
AN:
152222
Hom.:
63580
Cov.:
33
AF XY:
0.910
AC XY:
67701
AN XY:
74406
show subpopulations
Gnomad4 AFR
AF:
0.968
Gnomad4 AMR
AF:
0.893
Gnomad4 ASJ
AF:
0.885
Gnomad4 EAS
AF:
0.890
Gnomad4 SAS
AF:
0.920
Gnomad4 FIN
AF:
0.843
Gnomad4 NFE
AF:
0.899
Gnomad4 OTH
AF:
0.906
Alfa
AF:
0.906
Hom.:
58534
Bravo
AF:
0.920
Asia WGS
AF:
0.905
AC:
3144
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.69
DANN
Benign
0.47

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs10167992; hg19: chr2-263270; API