rs7191632

Variant names:

• chr16-4976483-T-C
• rs7191632
• NM_014692.2:c.64-11074T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

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

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 (EAS) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014692.2. 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
	SEC14L5	NM_014692.2	MANE Select	c.64-11074T>C		intron	N/A	NP_055507.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SEC14L5	ENST00000251170.12	TSL:1 MANE Select	c.64-11074T>C		intron	N/A	ENSP00000251170.6
	SEC14L5	ENST00000867654.1		c.64-11074T>C		intron	N/A	ENSP00000537713.1
	SEC14L5	ENST00000945616.1		c.64-11074T>C		intron	N/A	ENSP00000615675.1

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

African (AFR) AF: 0.553 AC: 22953 AN: 41510

American (AMR) AF: 0.553 AC: 8440 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1823 AN: 3466

East Asian (EAS) AF: 0.712 AC: 3675 AN: 5164

South Asian (SAS) AF: 0.706 AC: 3401 AN: 4820

European-Finnish (FIN) AF: 0.560 AC: 5913 AN: 10566

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.560 AC: 38061 AN: 67972

Other (OTH) AF: 0.576 AC: 1218 AN: 2114

Alfa AF: 0.563 Hom.: 75719

Bravo AF: 0.561

Asia WGS AF: 0.702 AC: 2443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.24
DANN	Benign	0.85
PhyloP100		-2.3
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: rs7191632; hg19: chr16-5026484;