rs1419832

Positions:

• chr10-116910771-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
SHTN1	NM_001127211.3	c.1359+1019T>C		intron_variant		ENST00000355371.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SHTN1	ENST00000355371.9	c.1359+1019T>C		intron_variant		2	NM_001127211.3	P1

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

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.634

Gnomad4 ASJ AF: 0.730

Gnomad4 EAS AF: 0.489

Gnomad4 SAS AF: 0.655

Gnomad4 FIN AF: 0.755

Gnomad4 NFE AF: 0.741

Gnomad4 OTH AF: 0.632

Alfa AF: 0.648 Hom.: 8749

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs1419832; hg19: chr10-118670282;