22-19750098-T-C

Variant names:

• chr22-19750098-T-C
• rs5993820

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 0.668 in 151,958 control chromosomes in the GnomAD database, including 34,059 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 0.67 (34059 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.719 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: 0.668 AC: 101433 AN: 151840 Hom.: 34024 Cov.: 33

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.668 AC: 101528 AN: 151958 Hom.: 34059 Cov.: 33 AF XY: 0.664 AC XY: 49324 AN XY: 74248

Gnomad4 AFR AF: 0.725

Gnomad4 AMR AF: 0.637

Gnomad4 ASJ AF: 0.701

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.701

Gnomad4 FIN AF: 0.585

Gnomad4 NFE AF: 0.658

Gnomad4 OTH AF: 0.657

Alfa AF: 0.664 Hom.: 46223

Bravo AF: 0.674

Asia WGS AF: 0.625 AC: 2175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.3
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5993820; hg19: chr22-19737621; COSMIC: COSV60107268;