chr19-44951429-T-C

Variant names:

• chr19-44951429-T-C
• rs7248162
• ENST00000591646.1:n.114-403A>G

Variant summary

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

The ENST00000591646.1(ENSG00000267114):​n.114-403A>G 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 151,826 control chromosomes in the GnomAD database, including 21,340 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 (21340 hom., cov: 31)
• Consequence: ENSG00000267114 ENST00000591646.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.542
• Publications: 9 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000591646.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000267114	ENST00000591646.1	TSL:3	n.114-403A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79241 AN: 151706 Hom.: 21305 Cov.: 31

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.522 AC: 79324 AN: 151826 Hom.: 21340 Cov.: 31 AF XY: 0.525 AC XY: 38935 AN XY: 74206

African (AFR) AF: 0.620 AC: 25642 AN: 41378

American (AMR) AF: 0.576 AC: 8790 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1572 AN: 3470

East Asian (EAS) AF: 0.553 AC: 2848 AN: 5150

South Asian (SAS) AF: 0.584 AC: 2813 AN: 4818

European-Finnish (FIN) AF: 0.489 AC: 5141 AN: 10524

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

European-Non Finnish (NFE) AF: 0.456 AC: 30951 AN: 67920

Other (OTH) AF: 0.502 AC: 1060 AN: 2112

Alfa AF: 0.553 Hom.: 5255

Bravo AF: 0.534

Asia WGS AF: 0.580 AC: 2016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.3
DANN	Benign	0.58
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs7248162; hg19: chr19-45454686;