20-19019182-G-T

Variant names:

• chr20-19019182-G-T
• rs6045766
• ENST00000617956.1:n.470-8666C>A

Variant summary

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

The ENST00000815938.1(ENSG00000306163):​n.145-29588G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 152,022 control chromosomes in the GnomAD database, including 31,401 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 0.64 (31401 hom., cov: 32)
• Consequence: ENSG00000306163 ENST00000815938.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 3 publications found

Genes affected

ENSG00000274863 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000815938.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000274863	ENST00000617956.1	TSL:5	n.470-8666C>A		intron	N/A
	ENSG00000306163	ENST00000815938.1		n.145-29588G>T		intron	N/A
	ENSG00000306163	ENST00000815939.1		n.134-24042G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96980 AN: 151904 Hom.: 31338 Cov.: 32

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.714

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.639 AC: 97106 AN: 152022 Hom.: 31401 Cov.: 32 AF XY: 0.648 AC XY: 48171 AN XY: 74334

African (AFR) AF: 0.630 AC: 26110 AN: 41438

American (AMR) AF: 0.714 AC: 10920 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2110 AN: 3468

East Asian (EAS) AF: 0.790 AC: 4083 AN: 5168

South Asian (SAS) AF: 0.677 AC: 3261 AN: 4818

European-Finnish (FIN) AF: 0.741 AC: 7837 AN: 10574

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.601 AC: 40822 AN: 67956

Other (OTH) AF: 0.621 AC: 1311 AN: 2110

Alfa AF: 0.614 Hom.: 110300

Bravo AF: 0.636

Asia WGS AF: 0.699 AC: 2430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.26
DANN	Benign	0.21
PhyloP100		-1.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6045766;

hg19: chr20-18999826;