10-116969480-T-C

Variant names:

• chr10-116969480-T-C
• rs2118207
• NM_001127211.3:c.112-768A>G

Variant summary

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

The NM_001127211.3(SHTN1):​c.112-768A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 152,042 control chromosomes in the GnomAD database, including 14,617 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 0.40 (14617 hom., cov: 32)
• Consequence: SHTN1 NM_001127211.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87
• Publications: 6 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SHTN1	NM_001127211.3	c.112-768A>G		intron_variant	Intron 2 of 16	ENST00000355371.9	NP_001120683.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SHTN1	ENST00000355371.9	c.112-768A>G		intron_variant	Intron 2 of 16	2	NM_001127211.3	ENSP00000347532.4

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60230 AN: 151924 Hom.: 14579 Cov.: 32

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.397 AC: 60318 AN: 152042 Hom.: 14617 Cov.: 32 AF XY: 0.393 AC XY: 29211 AN XY: 74300

African (AFR) AF: 0.682 AC: 28282 AN: 41448

American (AMR) AF: 0.360 AC: 5495 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 856 AN: 3468

East Asian (EAS) AF: 0.529 AC: 2732 AN: 5160

South Asian (SAS) AF: 0.359 AC: 1730 AN: 4818

European-Finnish (FIN) AF: 0.243 AC: 2573 AN: 10580

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17611 AN: 67968

Other (OTH) AF: 0.364 AC: 769 AN: 2110

Alfa AF: 0.271 Hom.: 2521

Bravo AF: 0.421

Asia WGS AF: 0.467 AC: 1624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0040
DANN	Benign	0.20
PhyloP100		-1.9
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2118207; hg19: chr10-118728991;