NM_001386936.1:c.3104+1320A>T

Variant names:

• chr14-71673942-A-T
• rs4902942
• NM_001386936.1:c.3104+1320A>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.3104+1320A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.838 in 152,226 control chromosomes in the GnomAD database, including 54,005 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 0.84 (54005 hom., cov: 31)
• Consequence: SIPA1L1 NM_001386936.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210
• Publications: 1 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.946 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.3104+1320A>T		intron	N/A	NP_001373865.1	O43166-2
	SIPA1L1	NM_001354285.2		c.3104+1320A>T		intron	N/A	NP_001341214.1	O43166-1
	SIPA1L1	NM_015556.4		c.3104+1320A>T		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.3104+1320A>T		intron	N/A	ENSP00000370630.3	O43166-2
	SIPA1L1	ENST00000555818.5	TSL:1	c.3104+1320A>T		intron	N/A	ENSP00000450832.1	O43166-1
	SIPA1L1	ENST00000962884.1		c.3104+1320A>T		intron	N/A	ENSP00000632943.1

Frequencies

GnomAD3 genomes AF: 0.837 AC: 127370 AN: 152108 Hom.: 53931 Cov.: 31

Gnomad AFR AF: 0.953

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.841

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.870

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.838 AC: 127507 AN: 152226 Hom.: 54005 Cov.: 31 AF XY: 0.842 AC XY: 62662 AN XY: 74420

African (AFR) AF: 0.954 AC: 39618 AN: 41546

American (AMR) AF: 0.842 AC: 12881 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.744 AC: 2582 AN: 3472

East Asian (EAS) AF: 0.937 AC: 4852 AN: 5176

South Asian (SAS) AF: 0.870 AC: 4197 AN: 4824

European-Finnish (FIN) AF: 0.837 AC: 8870 AN: 10594

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.765 AC: 52020 AN: 67994

Other (OTH) AF: 0.803 AC: 1697 AN: 2114

Alfa AF: 0.818 Hom.: 6380

Bravo AF: 0.840

Asia WGS AF: 0.901 AC: 3130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.88
DANN	Benign	0.36
PhyloP100		-0.021
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: rs4902942; hg19: chr14-72140659;