chr22-20674658-T-C

Variant names:

• chr22-20674658-T-C
• rs565979

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 0.54 in 151,988 control chromosomes in the GnomAD database, including 22,379 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 0.54 (22379 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.61 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: 0.540 AC: 82000 AN: 151870 Hom.: 22379 Cov.: 32

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.540 AC: 82038 AN: 151988 Hom.: 22379 Cov.: 32 AF XY: 0.547 AC XY: 40609 AN XY: 74296

Gnomad4 AFR AF: 0.480

Gnomad4 AMR AF: 0.488

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.490

Gnomad4 SAS AF: 0.629

Gnomad4 FIN AF: 0.714

Gnomad4 NFE AF: 0.560

Gnomad4 OTH AF: 0.517

Alfa AF: 0.560 Hom.: 12689

Bravo AF: 0.518

Asia WGS AF: 0.553 AC: 1925 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.091
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs565979; hg19: chr22-21028946;