chr20-17141948-A-G

Variant names:

• chr20-17141948-A-G
• rs852069
• ENST00000785117.1:n.323+6816A>G

Variant summary

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

The ENST00000785117.1(ENSG00000302234):​n.323+6816A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 151,956 control chromosomes in the GnomAD database, including 24,759 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 0.56 (24759 hom., cov: 32)
• Consequence: ENSG00000302234 ENST00000785117.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 31 publications found

Genes affected

ENSG00000302234 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372544	XR_937288.2	n.310+6816A>G		intron_variant	Intron 2 of 2
LOC105372544	XR_937289.1	n.310+6816A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302234	ENST00000785117.1	n.323+6816A>G		intron_variant	Intron 2 of 2
ENSG00000302234	ENST00000785118.1	n.266+6816A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85420 AN: 151838 Hom.: 24759 Cov.: 32

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.562 AC: 85438 AN: 151956 Hom.: 24759 Cov.: 32 AF XY: 0.559 AC XY: 41540 AN XY: 74286

African (AFR) AF: 0.493 AC: 20443 AN: 41434

American (AMR) AF: 0.532 AC: 8112 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 2235 AN: 3464

East Asian (EAS) AF: 0.219 AC: 1128 AN: 5158

South Asian (SAS) AF: 0.365 AC: 1760 AN: 4818

European-Finnish (FIN) AF: 0.673 AC: 7121 AN: 10584

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.631 AC: 42864 AN: 67926

Other (OTH) AF: 0.595 AC: 1256 AN: 2112

Alfa AF: 0.603 Hom.: 115457

Bravo AF: 0.550

Asia WGS AF: 0.339 AC: 1182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.7
DANN	Benign	0.65
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs852069; hg19: chr20-17122593;