chr20-48383513-A-C

Variant names:

• chr20-48383513-A-C
• rs2296090
• ENST00000446280.2:n.660-43T>G

Variant summary

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

The ENST00000446280.2(ENSG00000236874):​n.660-43T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 145,566 control chromosomes in the GnomAD database, including 2,624 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 0.16 (2624 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000236874 ENST00000446280.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.459
• Publications: 3 publications found

Genes affected

ENSG00000236874 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.372 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
ENSG00000236874	ENST00000446280.2	n.660-43T>G		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23027 AN: 145458 Hom.: 2618 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.0767

Gnomad SAS AF: 0.0998

Gnomad FIN AF: 0.0802

Gnomad MID AF: 0.0948

Gnomad NFE AF: 0.0838

Gnomad OTH AF: 0.135

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.158 AC: 23063 AN: 145566 Hom.: 2624 Cov.: 32 AF XY: 0.157 AC XY: 11164 AN XY: 71290

African (AFR) AF: 0.378 AC: 13339 AN: 35322

American (AMR) AF: 0.104 AC: 1554 AN: 14944

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 396 AN: 3472

East Asian (EAS) AF: 0.0771 AC: 400 AN: 5190

South Asian (SAS) AF: 0.0990 AC: 477 AN: 4818

European-Finnish (FIN) AF: 0.0802 AC: 852 AN: 10622

Middle Eastern (MID) AF: 0.0986 AC: 28 AN: 284

European-Non Finnish (NFE) AF: 0.0838 AC: 5695 AN: 67968

Other (OTH) AF: 0.133 AC: 271 AN: 2034

Alfa AF: 0.139 Hom.: 2291

Bravo AF: 0.161

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.6
DANN	Benign	0.86
PhyloP100		0.46
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2296090; hg19: chr20-47012256;