19-53719570-T-C

Variant names:

• chr19-53719570-T-C
• rs9304754
• ENST00000710708.1:n.585+6469T>C

Variant summary

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

The ENST00000710708.1(ENSG00000269842):​n.585+6469T>C variant causes a intron 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: ENSG00000269842 ENST00000710708.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.877
• Publications: 7 publications found

Genes affected

ENSG00000269842 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000269842	ENST00000710708.1	n.585+6469T>C		intron_variant	Intron 4 of 9

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

African (AFR) AF: 0.924 AC: 38342 AN: 41490

American (AMR) AF: 0.662 AC: 10082 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.797 AC: 2767 AN: 3470

East Asian (EAS) AF: 0.795 AC: 4099 AN: 5158

South Asian (SAS) AF: 0.682 AC: 3282 AN: 4812

European-Finnish (FIN) AF: 0.711 AC: 7493 AN: 10546

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.732 AC: 49752 AN: 67954

Other (OTH) AF: 0.763 AC: 1612 AN: 2112

Alfa AF: 0.746 Hom.: 180934

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
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs9304754; hg19: chr19-54222824;