1-232503516-T-A

Variant names:

• chr1-232503516-T-A
• rs720806
• NM_020808.5:c.1484-9856A>T

Variant summary

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

The NM_020808.5(SIPA1L2):​c.1484-9856A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 152,084 control chromosomes in the GnomAD database, including 14,188 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 0.41 (14188 hom., cov: 32)
• Consequence: SIPA1L2 NM_020808.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.186
• Publications: 1 publications found

Genes affected

SIPA1L2 (HGNC:23800): (signal induced proliferation associated 1 like 2) This gene encodes a member of the signal-induced proliferation-associated 1 like family. Members of this family contain a GTPase activating domain, a PDZ domain and a C-terminal coiled-coil domain with a leucine zipper. A similar protein in rat acts as a GTPases for the small GTPase Rap. [provided by RefSeq, Sep 2015]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.831 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020808.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SIPA1L2	NM_020808.5	MANE Select	c.1484-9856A>T		intron	N/A	NP_065859.3
	SIPA1L2	NM_001377488.1		c.1484-9856A>T		intron	N/A	NP_001364417.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SIPA1L2	ENST00000674635.1	MANE Select	c.1484-9856A>T		intron	N/A	ENSP00000502693.1
	SIPA1L2	ENST00000676213.1		c.1484-9856A>T		intron	N/A	ENSP00000501897.1
	SIPA1L2	ENST00000366630.5	TSL:5	c.1484-9856A>T		intron	N/A	ENSP00000355589.1

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61893 AN: 151966 Hom.: 14157 Cov.: 32

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.853

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.408 AC: 61983 AN: 152084 Hom.: 14188 Cov.: 32 AF XY: 0.416 AC XY: 30896 AN XY: 74340

African (AFR) AF: 0.524 AC: 21745 AN: 41466

American (AMR) AF: 0.505 AC: 7718 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1098 AN: 3468

East Asian (EAS) AF: 0.852 AC: 4400 AN: 5162

South Asian (SAS) AF: 0.445 AC: 2148 AN: 4824

European-Finnish (FIN) AF: 0.315 AC: 3330 AN: 10584

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20200 AN: 67974

Other (OTH) AF: 0.414 AC: 874 AN: 2112

Alfa AF: 0.356 Hom.: 1272

Bravo AF: 0.431

Asia WGS AF: 0.655 AC: 2275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.77
PhyloP100		0.19
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: rs720806; hg19: chr1-232639262;