19-53719570-T-C

Position:

• chr19-53719570-T-C

Variant summary

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

The ENST00000710708.1(ENSG00000269842):​n.585+6469T>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 0.779 in 151,980 control chromosomes in the GnomAD database, including 46,837 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 0.78 (46837 hom., cov: 31)
• Consequence: ENST00000710708.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.877

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.916 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
	ENST00000710708.1	n.585+6469T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.779 AC: 118247 AN: 151862 Hom.: 46793 Cov.: 31

Gnomad AFR AF: 0.924

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.797

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.779 AC: 118349 AN: 151980 Hom.: 46837 Cov.: 31 AF XY: 0.772 AC XY: 57372 AN XY: 74272

Gnomad4 AFR AF: 0.924

Gnomad4 AMR AF: 0.662

Gnomad4 ASJ AF: 0.797

Gnomad4 EAS AF: 0.795

Gnomad4 SAS AF: 0.682

Gnomad4 FIN AF: 0.711

Gnomad4 NFE AF: 0.732

Gnomad4 OTH AF: 0.763

Alfa AF: 0.738 Hom.: 85461

Bravo AF: 0.785

Asia WGS AF: 0.781 AC: 2717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	1.0
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9304754; hg19: chr19-54222824;