chr19-4361994-GTT-G

Position:

• chr19-4361994-GTT-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_003025.4(SH3GL1):​c.911-200_911-199delAA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.57 (25148 hom., cov: 0)
• Consequence: SH3GL1 NM_003025.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.587

Genes affected

SH3GL1 (HGNC:10830): (SH3 domain containing GRB2 like 1, endophilin A2) This gene encodes a member of the endophilin family of Src homology 3 domain-containing proteins. The encoded protein is involved in endocytosis and may also play a role in the cell cycle. Overexpression of this gene may play a role in leukemogenesis, and the encoded protein has been implicated in acute myeloid leukemia as a fusion partner of the myeloid-lymphoid leukemia protein. Pseudogenes of this gene are located on the long arm of chromosomes 11 and 17. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jan 2011]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 19-4361994-GTT-G is Benign according to our data. Variant chr19-4361994-GTT-G is described in ClinVar as [Benign]. Clinvar id is 1273325.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SH3GL1	NM_003025.4	c.911-200_911-199delAA		intron_variant		ENST00000269886.7	NP_003016.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SH3GL1	ENST00000269886.7	c.911-200_911-199delAA		intron_variant		1	NM_003025.4	ENSP00000269886.2
SH3GL1	ENST00000417295.6	c.767-200_767-199delAA		intron_variant		2		ENSP00000404568.2
SH3GL1	ENST00000598564.5	c.719-200_719-199delAA		intron_variant		2		ENSP00000470792.1

Frequencies

GnomAD3 genomes AF: 0.572 AC: 86835 AN: 151834 Hom.: 25101 Cov.: 0

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.602

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.572 AC: 86936 AN: 151952 Hom.: 25148 Cov.: 0 AF XY: 0.575 AC XY: 42678 AN XY: 74274

Gnomad4 AFR AF: 0.614

Gnomad4 AMR AF: 0.670

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.729

Gnomad4 SAS AF: 0.592

Gnomad4 FIN AF: 0.505

Gnomad4 NFE AF: 0.522

Gnomad4 OTH AF: 0.600

Alfa AF: 0.383 Hom.: 866

Bravo AF: 0.586

Asia WGS AF: 0.674 AC: 2343 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs61192422; hg19: chr19-4361991;