19-50501497-A-G

Position:

• chr19-50501497-A-G

Variant summary

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

The ENST00000702920.1(ENSG00000289950):​n.30+366T>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 0.756 in 152,096 control chromosomes in the GnomAD database, including 44,288 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 0.76 (44288 hom., cov: 34)
• Consequence: ENST00000702920.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000702920.1	n.30+366T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.756 AC: 114864 AN: 151978 Hom.: 44227 Cov.: 34

Gnomad AFR AF: 0.918

Gnomad AMI AF: 0.772

Gnomad AMR AF: 0.779

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.767

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

GnomAD4 genome AF: 0.756 AC: 114982 AN: 152096 Hom.: 44288 Cov.: 34 AF XY: 0.757 AC XY: 56249 AN XY: 74332

Gnomad4 AFR AF: 0.918

Gnomad4 AMR AF: 0.779

Gnomad4 ASJ AF: 0.676

Gnomad4 EAS AF: 0.697

Gnomad4 SAS AF: 0.755

Gnomad4 FIN AF: 0.667

Gnomad4 NFE AF: 0.674

Gnomad4 OTH AF: 0.766

Alfa AF: 0.685 Hom.: 54806

Bravo AF: 0.769

Asia WGS AF: 0.742 AC: 2583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.24
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1298062; hg19: chr19-51004754;