20-6423795-A-T

Variant names:

• chr20-6423795-A-T
• rs5005940

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 0.332 in 152,070 control chromosomes in the GnomAD database, including 8,649 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 0.33 (8649 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.349 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: 0.332 AC: 50428 AN: 151958 Hom.: 8649 Cov.: 32

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.0945

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.332 AC: 50449 AN: 152070 Hom.: 8649 Cov.: 32 AF XY: 0.329 AC XY: 24457 AN XY: 74338

African (AFR) AF: 0.349 AC: 14491 AN: 41474

American (AMR) AF: 0.305 AC: 4662 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1133 AN: 3470

East Asian (EAS) AF: 0.0948 AC: 491 AN: 5182

South Asian (SAS) AF: 0.309 AC: 1485 AN: 4812

European-Finnish (FIN) AF: 0.288 AC: 3045 AN: 10560

Middle Eastern (MID) AF: 0.336 AC: 98 AN: 292

European-Non Finnish (NFE) AF: 0.352 AC: 23953 AN: 67972

Other (OTH) AF: 0.327 AC: 692 AN: 2114

Alfa AF: 0.218 Hom.: 514

Bravo AF: 0.330

Asia WGS AF: 0.247 AC: 858 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.0
DANN	Benign	0.40
PhyloP100		-0.067

Splicing

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

Other links and lift over

dbSNP: rs5005940; hg19: chr20-6404442;