NM_001258300.1:c.-123+30585G>A

Variant names:

• chr10-117017860-C-T
• rs10787738
• NM_001258300.1:c.-123+30585G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001258300.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SHTN1	NM_001258300.1		c.-123+30585G>A		intron	N/A	NP_001245229.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SHTN1	ENST00000392901.10	TSL:2	c.-123+30585G>A		intron	N/A	ENSP00000376635.4

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

African (AFR) AF: 0.397 AC: 16428 AN: 41408

American (AMR) AF: 0.330 AC: 5034 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 853 AN: 3470

East Asian (EAS) AF: 0.508 AC: 2621 AN: 5162

South Asian (SAS) AF: 0.354 AC: 1703 AN: 4812

European-Finnish (FIN) AF: 0.245 AC: 2572 AN: 10518

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17687 AN: 67972

Other (OTH) AF: 0.305 AC: 643 AN: 2110

Alfa AF: 0.291 Hom.: 2620

Bravo AF: 0.327

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.65
PhyloP100		-0.45
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10787738; hg19: chr10-118777371;