ENST00000589999.1:n.109+16755C>T

Variant names:

• chr19-28615865-G-A
• rs6508962
• ENST00000589999.1:n.109+16755C>T

Variant summary

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

The ENST00000589999.1(ENSG00000290606):​n.109+16755C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.734 in 151,412 control chromosomes in the GnomAD database, including 41,493 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 0.73 (41493 hom., cov: 28)
• Consequence: ENSG00000290606 ENST00000589999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.998
• Publications: 2 publications found

Genes affected

ENSG00000290606 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.837 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100420587	NR_110759.1	n.656+106705C>T		intron_variant	Intron 5 of 9
LOC124904681	XR_007067212.1	n.262+4859C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290606	ENST00000589999.1	n.109+16755C>T		intron_variant	Intron 1 of 1	1
ENSG00000290606	ENST00000592347.5	n.642+106705C>T		intron_variant	Intron 5 of 9	1
ENSG00000290606	ENST00000585394.1	n.21-13322C>T		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.733 AC: 110963 AN: 151300 Hom.: 41425 Cov.: 28

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.794

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.734 AC: 111090 AN: 151412 Hom.: 41493 Cov.: 28 AF XY: 0.730 AC XY: 54016 AN XY: 73966

African (AFR) AF: 0.844 AC: 34815 AN: 41242

American (AMR) AF: 0.794 AC: 12079 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.674 AC: 2340 AN: 3472

East Asian (EAS) AF: 0.517 AC: 2652 AN: 5130

South Asian (SAS) AF: 0.461 AC: 2210 AN: 4790

European-Finnish (FIN) AF: 0.721 AC: 7505 AN: 10414

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47052 AN: 67840

Other (OTH) AF: 0.733 AC: 1544 AN: 2106

Alfa AF: 0.698 Hom.: 59203

Bravo AF: 0.747

Asia WGS AF: 0.553 AC: 1926 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	2.3
DANN	Benign	0.50
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs6508962; hg19: chr19-29106772;