19-48649698-G-A

Variant names:

• chr19-48649698-G-A
• rs8111500
• ENST00000474419.5:n.76+11552G>A

Variant summary

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

The ENST00000474419.5(SEC1P):​n.76+11552G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 152,106 control chromosomes in the GnomAD database, including 11,702 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 0.39 (11702 hom., cov: 33)
• Consequence: SEC1P ENST00000474419.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193
• Publications: 16 publications found

Genes affected

SEC1P (HGNC:):

SEC1P (HGNC:44149): (secretory blood group 1, pseudogene) Predicted to enable galactoside 2-alpha-L-fucosyltransferase activity. Predicted to act upstream of or within protein glycosylation. [provided by Alliance of Genome Resources, Apr 2022]

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 = 0.547 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SEC1P	NR_004401.2	n.108+11552G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SEC1P	ENST00000474419.5	n.76+11552G>A		intron_variant	Intron 1 of 3	1
SEC1P	ENST00000483163.1	n.76+11552G>A		intron_variant	Intron 1 of 1	1
SEC1P	ENST00000430145.3	n.48+11552G>A		intron_variant	Intron 1 of 4	2
SEC1P	ENST00000843316.1	n.48+11552G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59247 AN: 151988 Hom.: 11686 Cov.: 33

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.390 AC: 59304 AN: 152106 Hom.: 11702 Cov.: 33 AF XY: 0.391 AC XY: 29077 AN XY: 74358

African (AFR) AF: 0.393 AC: 16318 AN: 41472

American (AMR) AF: 0.359 AC: 5492 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1202 AN: 3470

East Asian (EAS) AF: 0.564 AC: 2922 AN: 5184

South Asian (SAS) AF: 0.380 AC: 1835 AN: 4824

European-Finnish (FIN) AF: 0.399 AC: 4214 AN: 10574

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.384 AC: 26123 AN: 67988

Other (OTH) AF: 0.381 AC: 803 AN: 2110

Alfa AF: 0.382 Hom.: 28132

Bravo AF: 0.386

Asia WGS AF: 0.464 AC: 1615 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.53
PhyloP100		0.19

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs8111500; hg19: chr19-49152955;