19-44951502-A-G

Position:

• chr19-44951502-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000591646.1(ENSG00000267114):​n.114-476T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 151,576 control chromosomes in the GnomAD database, including 20,042 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 0.51 (20042 hom., cov: 30)
• Consequence: ENST00000591646.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000591646.1	n.114-476T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77057 AN: 151456 Hom.: 20009 Cov.: 30

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.509 AC: 77138 AN: 151576 Hom.: 20042 Cov.: 30 AF XY: 0.511 AC XY: 37874 AN XY: 74066

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.445

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.580

Gnomad4 FIN AF: 0.487

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.491

Alfa AF: 0.377 Hom.: 1096

Bravo AF: 0.519

Asia WGS AF: 0.577 AC: 2007 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.092
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7247227; hg19: chr19-45454759; COSMIC: COSV52991016;