chr20-7279040-A-T

Variant names:

• chr20-7279040-A-T
• rs4239769

Variant summary

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

The variant allele was found at a frequency of 0.49 in 151,944 control chromosomes in the GnomAD database, including 18,927 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 0.49 (18927 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.6 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

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74408 AN: 151826 Hom.: 18891 Cov.: 32

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.490 AC: 74490 AN: 151944 Hom.: 18927 Cov.: 32 AF XY: 0.493 AC XY: 36572 AN XY: 74250

African (AFR) AF: 0.370 AC: 15330 AN: 41456

American (AMR) AF: 0.611 AC: 9322 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1971 AN: 3470

East Asian (EAS) AF: 0.429 AC: 2209 AN: 5154

South Asian (SAS) AF: 0.524 AC: 2524 AN: 4814

European-Finnish (FIN) AF: 0.468 AC: 4940 AN: 10554

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.537 AC: 36449 AN: 67926

Other (OTH) AF: 0.531 AC: 1117 AN: 2102

Alfa AF: 0.507 Hom.: 2479

Bravo AF: 0.494

Asia WGS AF: 0.508 AC: 1761 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.1
DANN	Benign	0.79
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs4239769; hg19: chr20-7259687;