20-24859528-A-G

Variant names:

• chr20-24859528-A-G
• rs11700219
• ENST00000776975.1:n.118-36036T>C

Variant summary

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

The ENST00000776975.1(ENSG00000301203):​n.118-36036T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.052 in 152,332 control chromosomes in the GnomAD database, including 372 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 0.052 (372 hom., cov: 32)
• Consequence: ENSG00000301203 ENST00000776975.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.331
• Publications: 0 publications found

Genes affected

ENSG00000301203 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.177 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
ENSG00000301203	ENST00000776975.1	n.118-36036T>C		intron_variant	Intron 2 of 4
ENSG00000301203	ENST00000776976.1	n.60+35983T>C		intron_variant	Intron 1 of 3
ENSG00000301203	ENST00000776977.1	n.261+12860T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0520 AC: 7917 AN: 152214 Hom.: 369 Cov.: 32

Gnomad AFR AF: 0.0114

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.0569

Gnomad FIN AF: 0.0634

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0489

Gnomad OTH AF: 0.0387

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

GnomAD4 genome AF: 0.0520 AC: 7924 AN: 152332 Hom.: 372 Cov.: 32 AF XY: 0.0548 AC XY: 4081 AN XY: 74488

African (AFR) AF: 0.0114 AC: 473 AN: 41586

American (AMR) AF: 0.128 AC: 1955 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0199 AC: 69 AN: 3472

East Asian (EAS) AF: 0.187 AC: 967 AN: 5184

South Asian (SAS) AF: 0.0567 AC: 274 AN: 4830

European-Finnish (FIN) AF: 0.0634 AC: 673 AN: 10620

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0489 AC: 3329 AN: 68018

Other (OTH) AF: 0.0397 AC: 84 AN: 2114

Alfa AF: 0.0515 Hom.: 520

Bravo AF: 0.0547

Asia WGS AF: 0.124 AC: 430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.9
DANN	Benign	0.66
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs11700219; hg19: chr20-24840164;