chr19-20478202-G-T

Variant names:

• chr19-20478202-G-T
• rs11666947
• ENST00000598131.1:n.257-18880G>T

Variant summary

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

The ENST00000598131.1(ENSG00000269043):​n.257-18880G>T variant causes a intron change. The variant allele was found at a frequency of 0.116 in 147,170 control chromosomes in the GnomAD database, including 1,788 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 0.12 (1788 hom., cov: 29)
• Consequence: ENSG00000269043 ENST00000598131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 4 publications found

Genes affected

ENSG00000269043 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000598131.1. 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
	ENSG00000269043	ENST00000598131.1	TSL:3	n.257-18880G>T		intron	N/A
	ENSG00000269043	ENST00000653011.1		n.201+5016G>T		intron	N/A
	ENSG00000269043	ENST00000737268.1		n.53+5016G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17089 AN: 147056 Hom.: 1792 Cov.: 29

Gnomad AFR AF: 0.0835

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.000619

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.0980

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.116 AC: 17080 AN: 147170 Hom.: 1788 Cov.: 29 AF XY: 0.115 AC XY: 8267 AN XY: 71632

African (AFR) AF: 0.0834 AC: 3323 AN: 39832

American (AMR) AF: 0.107 AC: 1568 AN: 14684

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 437 AN: 3340

East Asian (EAS) AF: 0.000621 AC: 3 AN: 4832

South Asian (SAS) AF: 0.117 AC: 495 AN: 4218

European-Finnish (FIN) AF: 0.160 AC: 1643 AN: 10298

Middle Eastern (MID) AF: 0.0876 AC: 24 AN: 274

European-Non Finnish (NFE) AF: 0.136 AC: 9106 AN: 66838

Other (OTH) AF: 0.106 AC: 213 AN: 2004

Alfa AF: 0.129 Hom.: 803

Asia WGS AF: 0.0560 AC: 197 AN: 3438

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.0
DANN	Benign	0.78

Splicing

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

Other links and lift over

dbSNP: rs11666947; hg19: chr19-20661008;