chr20-11194255-G-A

Variant names:

• chr20-11194255-G-A
• rs2207418
• ENST00000844940.1:n.99-22287G>A

Variant summary

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

The ENST00000844940.1(ENSG00000309883):​n.99-22287G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.732 in 152,122 control chromosomes in the GnomAD database, including 41,677 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 (41677 hom., cov: 33)
• Consequence: ENSG00000309883 ENST00000844940.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0860
• Publications: 16 publications found

Genes affected

ENSG00000309883 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 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
ENSG00000309883	ENST00000844940.1	n.99-22287G>A		intron_variant	Intron 1 of 1
ENSG00000309883	ENST00000844941.1	n.134-22287G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.732 AC: 111252 AN: 152004 Hom.: 41620 Cov.: 33

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.766

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.718

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

GnomAD4 genome AF: 0.732 AC: 111361 AN: 152122 Hom.: 41677 Cov.: 33 AF XY: 0.724 AC XY: 53823 AN XY: 74344

African (AFR) AF: 0.835 AC: 34681 AN: 41512

American (AMR) AF: 0.566 AC: 8656 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.745 AC: 2587 AN: 3472

East Asian (EAS) AF: 0.386 AC: 1996 AN: 5168

South Asian (SAS) AF: 0.650 AC: 3135 AN: 4820

European-Finnish (FIN) AF: 0.710 AC: 7502 AN: 10564

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.741 AC: 50359 AN: 67986

Other (OTH) AF: 0.723 AC: 1526 AN: 2112

Alfa AF: 0.726 Hom.: 136268

Bravo AF: 0.721

Asia WGS AF: 0.559 AC: 1942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.68
DANN	Benign	0.68
PhyloP100		0.086

Splicing

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

Other links and lift over

dbSNP: rs2207418; hg19: chr20-11174903;