20-46095024-C-T

Variant names:

• chr20-46095024-C-T
• rs11086996
• ENST00000758803.1:n.364-1262G>A

Variant summary

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

The ENST00000758803.1(ENSG00000298900):​n.364-1262G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,042 control chromosomes in the GnomAD database, including 3,088 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 0.20 (3088 hom., cov: 32)
• Consequence: ENSG00000298900 ENST00000758803.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790
• Publications: 15 publications found

Genes affected

ENSG00000298900 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.275 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
ENSG00000298900	ENST00000758803.1	n.364-1262G>A		intron_variant	Intron 2 of 2
ENSG00000298900	ENST00000758804.1	n.197-1262G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29842 AN: 151924 Hom.: 3081 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.0283

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.196 AC: 29871 AN: 152042 Hom.: 3088 Cov.: 32 AF XY: 0.197 AC XY: 14662 AN XY: 74324

African (AFR) AF: 0.178 AC: 7371 AN: 41462

American (AMR) AF: 0.202 AC: 3085 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 673 AN: 3472

East Asian (EAS) AF: 0.0282 AC: 146 AN: 5180

South Asian (SAS) AF: 0.288 AC: 1387 AN: 4816

European-Finnish (FIN) AF: 0.211 AC: 2231 AN: 10552

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14289 AN: 67962

Other (OTH) AF: 0.185 AC: 390 AN: 2112

Alfa AF: 0.204 Hom.: 5419

Bravo AF: 0.190

Asia WGS AF: 0.165 AC: 574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.88
DANN	Benign	0.24
PhyloP100		-0.079

Splicing

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

Other links and lift over

dbSNP: rs11086996; hg19: chr20-44723663;