1-154471733-T-C

Variant names:

• chr1-154471733-T-C
• rs7526293
• ENST00000486773.1:c.102-1371A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000486773.1(SHE):​c.102-1371A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.73 in 151,928 control chromosomes in the GnomAD database, including 41,225 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 0.73 (41225 hom., cov: 30)
• Consequence: SHE ENST00000486773.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.71
• Publications: 16 publications found

Genes affected

SHE (HGNC:27004): (Src homology 2 domain containing E) Predicted to enable phosphotyrosine residue binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000486773.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SHE	ENST00000486773.1	TSL:3	c.102-1371A>G		intron	N/A	ENSP00000452008.1	H0YJR4

Frequencies

GnomAD3 genomes AF: 0.730 AC: 110808 AN: 151810 Hom.: 41212 Cov.: 30

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.730 AC: 110857 AN: 151928 Hom.: 41225 Cov.: 30 AF XY: 0.725 AC XY: 53846 AN XY: 74230

African (AFR) AF: 0.586 AC: 24237 AN: 41370

American (AMR) AF: 0.810 AC: 12364 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.822 AC: 2851 AN: 3470

East Asian (EAS) AF: 0.833 AC: 4316 AN: 5182

South Asian (SAS) AF: 0.766 AC: 3690 AN: 4816

European-Finnish (FIN) AF: 0.653 AC: 6867 AN: 10516

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.793 AC: 53916 AN: 67990

Other (OTH) AF: 0.751 AC: 1582 AN: 2106

Alfa AF: 0.758 Hom.: 9782

Bravo AF: 0.738

Asia WGS AF: 0.755 AC: 2626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.073
DANN	Benign	0.55
PhyloP100		-3.7

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7526293; hg19: chr1-154444209;