20-6946722-A-G

Variant names:

• chr20-6946722-A-G
• rs6038661

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.85 in 152,222 control chromosomes in the GnomAD database, including 55,559 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 0.85 (55559 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.416

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.9 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: 0.850 AC: 129299 AN: 152104 Hom.: 55496 Cov.: 33

Gnomad AFR AF: 0.908

Gnomad AMI AF: 0.938

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.696

Gnomad FIN AF: 0.895

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.845

Gnomad OTH AF: 0.823

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

GnomAD4 genome AF: 0.850 AC: 129424 AN: 152222 Hom.: 55559 Cov.: 33 AF XY: 0.847 AC XY: 63060 AN XY: 74422

Gnomad4 AFR AF: 0.908

Gnomad4 AMR AF: 0.868

Gnomad4 ASJ AF: 0.780

Gnomad4 EAS AF: 0.498

Gnomad4 SAS AF: 0.698

Gnomad4 FIN AF: 0.895

Gnomad4 NFE AF: 0.845

Gnomad4 OTH AF: 0.820

Alfa AF: 0.841 Hom.: 24601

Bravo AF: 0.853

Asia WGS AF: 0.648 AC: 2253 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6038661; hg19: chr20-6927369;