chr19-44951106-G-A

Variant names:

• chr19-44951106-G-A
• rs11083752
• ENST00000591646.1:n.114-80C>T

Variant summary

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

The ENST00000591646.1(ENSG00000267114):​n.114-80C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 151,870 control chromosomes in the GnomAD database, including 21,328 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 0.52 (21317 hom., cov: 30)
  • Exomes 𝑓: 0.39 (11 hom.)
• Consequence: ENSG00000267114 ENST00000591646.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.151
• Publications: 8 publications found

Genes affected

ENSG00000267114 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.614 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
ENSG00000267114	ENST00000591646.1	n.114-80C>T		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79187 AN: 151646 Hom.: 21282 Cov.: 30

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.501

GnomAD4 exome AF: 0.394 AC: 41 AN: 104 Hom.: 11 AF XY: 0.378 AC XY: 31 AN XY: 82

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AF: 1.00 AC: 2 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.900 AC: 9 AN: 10

European-Finnish (FIN) AF: 0.375 AC: 3 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.289 AC: 22 AN: 76

Other (OTH) AF: 0.833 AC: 5 AN: 6

GnomAD4 genome AF: 0.522 AC: 79270 AN: 151766 Hom.: 21317 Cov.: 30 AF XY: 0.525 AC XY: 38890 AN XY: 74132

African (AFR) AF: 0.620 AC: 25616 AN: 41322

American (AMR) AF: 0.576 AC: 8794 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1554 AN: 3472

East Asian (EAS) AF: 0.553 AC: 2852 AN: 5154

South Asian (SAS) AF: 0.584 AC: 2810 AN: 4810

European-Finnish (FIN) AF: 0.488 AC: 5129 AN: 10500

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 30948 AN: 67936

Other (OTH) AF: 0.502 AC: 1058 AN: 2108

Alfa AF: 0.481 Hom.: 26403

Bravo AF: 0.534

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	7.5
DANN	Benign	0.76
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs11083752; hg19: chr19-45454363;