rs1419832

Variant names:

• chr10-116910771-A-G
• rs1419832
• NM_001127211.3:c.1359+1019T>C

Variant summary

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

The NM_001127211.3(SHTN1):​c.1359+1019T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 152,072 control chromosomes in the GnomAD database, including 29,991 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 0.60 (29991 hom., cov: 32)
• Consequence: SHTN1 NM_001127211.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.801
• Publications: 3 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]

ENO4 (HGNC:31670): (enolase 4) Predicted to enable phosphopyruvate hydratase activity. Predicted to be involved in glycolytic process and regulation of vacuole fusion, non-autophagic. Predicted to act upstream of or within cilium organization and flagellated sperm motility. Predicted to be located in sperm principal piece. Predicted to be part of phosphopyruvate hydratase complex. [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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SHTN1	NM_001127211.3	c.1359+1019T>C		intron_variant	Intron 14 of 16	ENST00000355371.9	NP_001120683.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SHTN1	ENST00000355371.9	c.1359+1019T>C		intron_variant	Intron 14 of 16	2	NM_001127211.3	ENSP00000347532.4

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90627 AN: 151954 Hom.: 29985 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.701

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.596 AC: 90652 AN: 152072 Hom.: 29991 Cov.: 32 AF XY: 0.599 AC XY: 44554 AN XY: 74330

African (AFR) AF: 0.292 AC: 12108 AN: 41474

American (AMR) AF: 0.634 AC: 9695 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.730 AC: 2534 AN: 3470

East Asian (EAS) AF: 0.489 AC: 2524 AN: 5166

South Asian (SAS) AF: 0.655 AC: 3155 AN: 4814

European-Finnish (FIN) AF: 0.755 AC: 7980 AN: 10572

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.741 AC: 50401 AN: 67978

Other (OTH) AF: 0.632 AC: 1335 AN: 2114

Alfa AF: 0.659 Hom.: 14065

Bravo AF: 0.570

Asia WGS AF: 0.538 AC: 1871 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.8
DANN	Benign	0.37
PhyloP100		-0.80
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: rs1419832; hg19: chr10-118670282;