chr10-117075480-C-T

Variant names:

• chr10-117075480-C-T
• rs4752028
• NM_001258300.1:c.-188-26970G>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.-188-26970G>A 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 152,112 control chromosomes in the GnomAD database, including 42,264 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 (42264 hom., cov: 33)
• Consequence: SHTN1 NM_001258300.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 19 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SHTN1	NM_001258300.1	c.-188-26970G>A		intron_variant	Intron 1 of 17		NP_001245229.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SHTN1	ENST00000392901.10	c.-188-26970G>A		intron_variant	Intron 1 of 17	2		ENSP00000376635.4

Frequencies

GnomAD3 genomes AF: 0.731 AC: 111032 AN: 151994 Hom.: 42249 Cov.: 33

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.897

Gnomad EAS AF: 0.661

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.841

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.834

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.730 AC: 111074 AN: 152112 Hom.: 42264 Cov.: 33 AF XY: 0.735 AC XY: 54656 AN XY: 74384

African (AFR) AF: 0.495 AC: 20522 AN: 41456

American (AMR) AF: 0.766 AC: 11715 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.897 AC: 3113 AN: 3472

East Asian (EAS) AF: 0.662 AC: 3419 AN: 5168

South Asian (SAS) AF: 0.851 AC: 4097 AN: 4816

European-Finnish (FIN) AF: 0.841 AC: 8915 AN: 10598

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.834 AC: 56704 AN: 68000

Other (OTH) AF: 0.756 AC: 1593 AN: 2108

Alfa AF: 0.803 Hom.: 204402

Bravo AF: 0.709

Asia WGS AF: 0.719 AC: 2503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.26
DANN	Benign	0.43
PhyloP100		-1.4
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: rs4752028; hg19: chr10-118834991;