rs2742435

Variant names:

• chr3-45699371-G-A
• rs2742435
• NM_014016.5:c.33-4067G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-45699371-G-A
• chr3-45699371-G-C

Variant summary

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

The NM_014016.5(SACM1L):​c.33-4067G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 150,980 control chromosomes in the GnomAD database, including 14,788 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 (14788 hom., cov: 33)
• Consequence: SACM1L NM_014016.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 3 publications found

Genes affected

SACM1L (HGNC:17059): (SAC1 like phosphatidylinositide phosphatase) This gene encodes an integral membrane protein, which is localized to the endoplasmic reticulum, and functions as a phosphoinositide phosphatase that hydrolyzes phosphatidylinositol 3-phosphate, phosphatidylinositol 4-phosphate, and phosphatidylinositol 3,5-bisphosphate. Deletion of this gene in mouse results in preimplantation lethality. Other studies suggest that this gene is also involved in the organization of golgi membranes and mitotic spindles. Alternatively spliced transcript variants have been found for this gene. A C-terminally extended isoform is also predicted to be produced by the use of an alternative in-frame, downstream translation termination codon via a stop codon readthrough mechanism.[provided by RefSeq, Dec 2017]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014016.5. 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
	SACM1L	NM_014016.5	MANE Select	c.33-4067G>A		intron	N/A	NP_054735.3
	SACM1L	NM_001319071.2		c.33-4067G>A		intron	N/A	NP_001306000.1	A0A5F9ZHN7
	SACM1L	NM_001319072.2		c.-23-4067G>A		intron	N/A	NP_001306001.1	Q9NTJ5-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SACM1L	ENST00000389061.10	TSL:1 MANE Select	c.33-4067G>A		intron	N/A	ENSP00000373713.4	Q9NTJ5-1
	SACM1L	ENST00000455997.5	TSL:1	n.-277-4067G>A		intron	N/A	ENSP00000389975.1	F8WDN7
	SACM1L	ENST00000672858.2		c.33-4067G>A		intron	N/A	ENSP00000500542.2	A0A5F9ZHN7

Frequencies

GnomAD3 genomes AF: 0.415 AC: 62542 AN: 150862 Hom.: 14778 Cov.: 33

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.414 AC: 62580 AN: 150980 Hom.: 14788 Cov.: 33 AF XY: 0.412 AC XY: 30391 AN XY: 73838

African (AFR) AF: 0.202 AC: 8376 AN: 41374

American (AMR) AF: 0.457 AC: 6957 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2098 AN: 3460

East Asian (EAS) AF: 0.190 AC: 983 AN: 5176

South Asian (SAS) AF: 0.327 AC: 1577 AN: 4822

European-Finnish (FIN) AF: 0.544 AC: 5388 AN: 9912

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.527 AC: 35652 AN: 67700

Other (OTH) AF: 0.449 AC: 941 AN: 2094

Alfa AF: 0.464 Hom.: 28924

Bravo AF: 0.403

Asia WGS AF: 0.275 AC: 950 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.61
DANN	Benign	0.10
PhyloP100		-1.0
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: rs2742435; hg19: chr3-45740863;