20-4675114-C-T

Variant names:

• chr20-4675114-C-T
• rs1029273
• ENST00000652447.1:n.87+9948G>A

Variant summary

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

The ENST00000652447.1(ENSG00000293214):​n.87+9948G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.602 in 151,986 control chromosomes in the GnomAD database, including 27,707 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 0.60 (27707 hom., cov: 32)
• Consequence: ENSG00000293214 ENST00000652447.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222
• Publications: 3 publications found

Genes affected

ENSG00000293214 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.648 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
ENSG00000293214	ENST00000652447.1	n.87+9948G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91334 AN: 151866 Hom.: 27659 Cov.: 32

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.593

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.602 AC: 91448 AN: 151986 Hom.: 27707 Cov.: 32 AF XY: 0.602 AC XY: 44747 AN XY: 74306

African (AFR) AF: 0.650 AC: 26942 AN: 41428

American (AMR) AF: 0.659 AC: 10072 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.562 AC: 1947 AN: 3464

East Asian (EAS) AF: 0.410 AC: 2123 AN: 5174

South Asian (SAS) AF: 0.505 AC: 2433 AN: 4818

European-Finnish (FIN) AF: 0.611 AC: 6451 AN: 10552

Middle Eastern (MID) AF: 0.592 AC: 173 AN: 292

European-Non Finnish (NFE) AF: 0.582 AC: 39525 AN: 67952

Other (OTH) AF: 0.601 AC: 1268 AN: 2110

Alfa AF: 0.606 Hom.: 18566

Bravo AF: 0.609

Asia WGS AF: 0.477 AC: 1660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.0
DANN	Benign	0.35
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs1029273; hg19: chr20-4655760;