NM_174975.5:c.*311G>T

Variant names:

• chr22-30459710-C-A
• rs5753158
• NM_174975.5:c.*311G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_174975.5(SEC14L3):​c.*311G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000111 in 900,918 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000011 (0 hom.)
• Consequence: SEC14L3 NM_174975.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.425
• Publications: 0 publications found

Genes affected

SEC14L3 (HGNC:18655): (SEC14 like lipid binding 3) The protein encoded by this gene is highly similar to the protein encoded by the Saccharomyces cerevisiae SEC14 gene. The SEC14 protein is a phophatidylinositol transfer protein that is essential for biogenesis of Golgi-derived transport vesicles, and thus is required for the export of yeast secretory proteins from the Golgi complex. The specific function of this protein has not yet been determined. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jul 2012]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_174975.5. 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
	SEC14L3	NM_174975.5	MANE Select	c.*311G>T		3_prime_UTR	Exon 12 of 12	NP_777635.1
	SEC14L3	NM_001257379.2		c.*311G>T		3_prime_UTR	Exon 13 of 13	NP_001244308.1
	SEC14L3	NM_001257382.2		c.*311G>T		3_prime_UTR	Exon 13 of 13	NP_001244311.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SEC14L3	ENST00000215812.9	TSL:1 MANE Select	c.*311G>T		3_prime_UTR	Exon 12 of 12	ENSP00000215812.5
	SEC14L3	ENST00000401751.5	TSL:1	c.*311G>T		3_prime_UTR	Exon 13 of 13	ENSP00000383896.1
	SEC14L3	ENST00000402286.5	TSL:1	c.*311G>T		3_prime_UTR	Exon 14 of 14	ENSP00000385004.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000111 AC: 1 AN: 900918 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 419390

African (AFR) AF: 0.00 AC: 0 AN: 19126

American (AMR) AF: 0.00 AC: 0 AN: 5872

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 7574

East Asian (EAS) AF: 0.00 AC: 0 AN: 9070

South Asian (SAS) AF: 0.00 AC: 0 AN: 20174

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2902

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1902

European-Non Finnish (NFE) AF: 0.00000125 AC: 1 AN: 802936

Other (OTH) AF: 0.00 AC: 0 AN: 31362

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.2
DANN	Benign	0.44
PhyloP100		0.42

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: rs5753158; hg19: chr22-30855697;