rs7191632

chr16-4976483-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014692.2(SEC14L5):c.64-11074T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 152,086 control chromosomes in the GnomAD database, including 24,466 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 0.57 (24466 hom., cov: 33)
• Consequence: SEC14L5 NM_014692.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26

Genes affected

SEC14L5 (HGNC:29032): (SEC14 like lipid binding 5)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SEC14L5	NM_014692.2	c.64-11074T>C		intron_variant		ENST00000251170.12
SEC14L5	XM_024450497.2	c.64-11074T>C		intron_variant
SEC14L5	XM_024450498.2	c.64-11074T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SEC14L5	ENST00000251170.12	c.64-11074T>C		intron_variant		1	NM_014692.2	P1
SEC14L5	ENST00000587469.1	c.64-11074T>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.566 AC: 85977 AN: 151968 Hom.: 24443 Cov.: 33

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.566 AC: 86057 AN: 152086 Hom.: 24466 Cov.: 33 AF XY: 0.568 AC XY: 42225 AN XY: 74326

Gnomad4 AFR AF: 0.553

Gnomad4 AMR AF: 0.553

Gnomad4 ASJ AF: 0.526

Gnomad4 EAS AF: 0.712

Gnomad4 SAS AF: 0.706

Gnomad4 FIN AF: 0.560

Gnomad4 NFE AF: 0.560

Gnomad4 OTH AF: 0.576

Alfa AF: 0.564 Hom.: 49442

Bravo AF: 0.561

Asia WGS AF: 0.702 AC: 2443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.24
Dann	Benign	0.85

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

Publications

LitVar

Other links and lift over

dbSNP: rs7191632; hg19: chr16-5026484;