rs10787738

chr10-117017860-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001258300.1(SHTN1):c.-123+30585G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 151,910 control chromosomes in the GnomAD database, including 7,972 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 0.31 (7972 hom., cov: 32)
• Consequence: SHTN1 NM_001258300.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.449

Genes affected

SHTN1 (HGNC:29319): (shootin 1) Enables identical protein binding activity. Involved in positive regulation of neuron migration. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.492 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SHTN1	NM_001258300.1	c.-123+30585G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SHTN1	ENST00000392901.10	c.-123+30585G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47764 AN: 151794 Hom.: 7965 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.315 AC: 47807 AN: 151910 Hom.: 7972 Cov.: 32 AF XY: 0.314 AC XY: 23295 AN XY: 74222

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.508

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.305

Alfa AF: 0.290 Hom.: 2108

Bravo AF: 0.327

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.0
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10787738; hg19: chr10-118777371;