19-48952744-C-T

Variant names:

• chr19-48952744-C-T
• rs11667229
• ENST00000812088.1:n.328-2419G>A

Variant summary

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

The ENST00000812088.1(ENSG00000305635):​n.328-2419G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 152,018 control chromosomes in the GnomAD database, including 17,199 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 0.46 (17199 hom., cov: 32)
• Consequence: ENSG00000305635 ENST00000812088.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 14 publications found

Genes affected

ENSG00000305635 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305635	ENST00000812088.1	n.328-2419G>A		intron_variant	Intron 1 of 1
ENSG00000305635	ENST00000812089.1	n.472-2419G>A		intron_variant	Intron 2 of 2
ENSG00000305635	ENST00000812090.1	n.273-2419G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69879 AN: 151900 Hom.: 17185 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.460 AC: 69928 AN: 152018 Hom.: 17199 Cov.: 32 AF XY: 0.466 AC XY: 34608 AN XY: 74296

African (AFR) AF: 0.264 AC: 10949 AN: 41494

American (AMR) AF: 0.489 AC: 7460 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1729 AN: 3470

East Asian (EAS) AF: 0.614 AC: 3172 AN: 5162

South Asian (SAS) AF: 0.539 AC: 2601 AN: 4824

European-Finnish (FIN) AF: 0.578 AC: 6094 AN: 10552

Middle Eastern (MID) AF: 0.500 AC: 146 AN: 292

European-Non Finnish (NFE) AF: 0.534 AC: 36308 AN: 67954

Other (OTH) AF: 0.486 AC: 1024 AN: 2106

Alfa AF: 0.513 Hom.: 32682

Bravo AF: 0.446

Asia WGS AF: 0.535 AC: 1859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.31
DANN	Benign	0.72
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs11667229; hg19: chr19-49456001;