chr20-40266247-A-T

Variant names:

• chr20-40266247-A-T
• rs5009524
• ENST00000807626.1:n.125+5199T>A

Variant summary

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

The ENST00000807626.1(ENSG00000305005):​n.125+5199T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 152,152 control chromosomes in the GnomAD database, including 6,804 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 0.30 (6804 hom., cov: 33)
• Consequence: ENSG00000305005 ENST00000807626.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.692
• Publications: 1 publications found

Genes affected

ENSG00000305005 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807626.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305005	ENST00000807626.1		n.125+5199T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44892 AN: 152034 Hom.: 6803 Cov.: 33

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.295 AC: 44919 AN: 152152 Hom.: 6804 Cov.: 33 AF XY: 0.295 AC XY: 21948 AN XY: 74386

African (AFR) AF: 0.313 AC: 12970 AN: 41496

American (AMR) AF: 0.233 AC: 3557 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1497 AN: 3472

East Asian (EAS) AF: 0.111 AC: 573 AN: 5178

South Asian (SAS) AF: 0.336 AC: 1616 AN: 4816

European-Finnish (FIN) AF: 0.312 AC: 3303 AN: 10600

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20394 AN: 67990

Other (OTH) AF: 0.296 AC: 625 AN: 2110

Alfa AF: 0.298 Hom.: 852

Bravo AF: 0.287

Asia WGS AF: 0.216 AC: 754 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.5
DANN	Benign	0.72
PhyloP100		0.69

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs5009524;

hg19: chr20-38894887;