rs11158907

Variant names:

• chr14-71520348-A-G
• rs11158907
• NM_001386936.1:c.-362+7503A>G

Your query was ambiguous. Multiple possible variants found:

• chr14-71520348-A-G
• chr14-71520348-A-T

Variant summary

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

The NM_001386936.1(SIPA1L1):​c.-362+7503A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,170 control chromosomes in the GnomAD database, including 1,570 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 0.12 (1570 hom., cov: 32)
• Consequence: SIPA1L1 NM_001386936.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.747
• Publications: 5 publications found

Genes affected

SIPA1L1 (HGNC:20284): (signal induced proliferation associated 1 like 1) Predicted to enable GTPase activator activity; actin filament binding activity; and protein kinase binding activity. Predicted to be involved in several processes, including actin cytoskeleton organization; activation of GTPase activity; and regulation of postsynapse organization. Located in actin cytoskeleton and plasma membrane. [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=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001386936.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SIPA1L1	NM_001386936.1	MANE Select	c.-362+7503A>G		intron	N/A	NP_001373865.1	O43166-2
	SIPA1L1	NM_001354285.2		c.-362+7503A>G		intron	N/A	NP_001341214.1	O43166-1
	SIPA1L1	NM_015556.4		c.-362+7503A>G		intron	N/A	NP_056371.1	O43166-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SIPA1L1	ENST00000381232.8	TSL:1 MANE Select	c.-362+7503A>G		intron	N/A	ENSP00000370630.3	O43166-2
	SIPA1L1	ENST00000962884.1		c.-362+7503A>G		intron	N/A	ENSP00000632943.1
	SIPA1L1	ENST00000869393.1		c.-362+7503A>G		intron	N/A	ENSP00000539452.1

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18735 AN: 152052 Hom.: 1568 Cov.: 32

Gnomad AFR AF: 0.0529

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.123 AC: 18743 AN: 152170 Hom.: 1570 Cov.: 32 AF XY: 0.126 AC XY: 9402 AN XY: 74380

African (AFR) AF: 0.0529 AC: 2197 AN: 41538

American (AMR) AF: 0.141 AC: 2151 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 880 AN: 3466

East Asian (EAS) AF: 0.413 AC: 2131 AN: 5160

South Asian (SAS) AF: 0.244 AC: 1177 AN: 4816

European-Finnish (FIN) AF: 0.106 AC: 1118 AN: 10592

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8694 AN: 67990

Other (OTH) AF: 0.142 AC: 299 AN: 2110

Alfa AF: 0.134 Hom.: 6611

Bravo AF: 0.124

Asia WGS AF: 0.295 AC: 1023 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	6.6
DANN	Benign	0.87
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs11158907; hg19: chr14-71987065;