Variant 2-256278-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001282687.2(SH3YL1):c.-493A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 152,238 control chromosomes in the GnomAD database, including 6,802 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 ( 6801 hom., cov: 33)

Exomes 𝑓: 0.40 ( 1 hom. )

Consequence

SH3YL1
NM_001282687.2 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.423

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]

SH3YL1 links:

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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 (EAS) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SH3YL1	NM_015677.4 link	c.2-3163A>G		intron_variant		ENST00000356150.10	NP_056492.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SH3YL1	ENST00000626873.2 link	c.-493A>G		5_prime_UTR_variant	2/13	5		ENSP00000485824.1		Q96HL8-3
SH3YL1	ENST00000356150.10 link	c.2-3163A>G		intron_variant		1	NM_015677.4	ENSP00000348471.5		Q96HL8-1

Frequencies

GnomAD3 genomes

AF:

0.274

AC:

41732

AN:

152110

Hom.:

6808

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0982

Gnomad AMI

AF:

0.257

Gnomad AMR

AF:

0.263

Gnomad ASJ

AF:

0.326

Gnomad EAS

AF:

0.527

Gnomad SAS

AF:

0.261

Gnomad FIN

AF:

0.398

Gnomad MID

AF:

0.339

Gnomad NFE

AF:

0.344

Gnomad OTH

AF:

0.281

GnomAD4 exome

AF:

0.400

AC:

AN:

Hom.:

Cov.:

AF XY:

0.333

AC XY:

AN XY:

show subpopulations

Gnomad4 SAS exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.500

GnomAD4 genome

AF:

0.274

AC:

41715

AN:

152228

Hom.:

6801

Cov.:

AF XY:

0.277

AC XY:

20598

AN XY:

74422

show subpopulations

Gnomad4 AFR

AF:

0.0980

Gnomad4 AMR

AF:

0.262

Gnomad4 ASJ

AF:

0.326

Gnomad4 EAS

AF:

0.527

Gnomad4 SAS

AF:

0.258

Gnomad4 FIN

AF:

0.398

Gnomad4 NFE

AF:

0.344

Gnomad4 OTH

AF:

0.279

Alfa

AF:

0.300

Hom.:

4115

Bravo

AF:

0.258

Asia WGS

AF:

0.319

AC:

1108

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

1.2

DANN

Benign

0.48

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over