rs78644782

Variant names:

• chr19-28599834-G-T
• rs78644782
• ENST00000589999.1:n.109+32786C>A

Variant summary

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

The ENST00000589999.1(ENSG00000290606):​n.109+32786C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0134 in 152,256 control chromosomes in the GnomAD database, including 88 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 0.013 (88 hom., cov: 32)
• Consequence: ENSG00000290606 ENST00000589999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100420587	NR_110759.1	n.656+122736C>A		intron_variant	Intron 5 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290606	ENST00000589999.1	n.109+32786C>A		intron_variant	Intron 1 of 1	1
ENSG00000290606	ENST00000592347.5	n.642+122736C>A		intron_variant	Intron 5 of 9	1
ENSG00000290606	ENST00000716069.1	n.177+40857C>A		intron_variant	Intron 2 of 6
ENSG00000290606	ENST00000716071.1	n.716-14478C>A		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.0134 AC: 2046 AN: 152138 Hom.: 88 Cov.: 32

Gnomad AFR AF: 0.000821

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00295

Gnomad ASJ AF: 0.00663

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.00684

Gnomad FIN AF: 0.0535

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00706

Gnomad OTH AF: 0.0105

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

GnomAD4 genome AF: 0.0134 AC: 2046 AN: 152256 Hom.: 88 Cov.: 32 AF XY: 0.0154 AC XY: 1143 AN XY: 74446

African (AFR) AF: 0.000818 AC: 34 AN: 41550

American (AMR) AF: 0.00294 AC: 45 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.00663 AC: 23 AN: 3468

East Asian (EAS) AF: 0.162 AC: 839 AN: 5168

South Asian (SAS) AF: 0.00705 AC: 34 AN: 4824

European-Finnish (FIN) AF: 0.0535 AC: 568 AN: 10614

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00706 AC: 480 AN: 68018

Other (OTH) AF: 0.0109 AC: 23 AN: 2108

Alfa AF: 0.0115 Hom.: 5

Bravo AF: 0.0105

Asia WGS AF: 0.0600 AC: 208 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	0.072
DANN	Benign	0.17
PhyloP100		0.089

Splicing

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

Other links and lift over

dbSNP: rs78644782; hg19: chr19-29090741;