rs41298629

chr22-19755950-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.0376 in 152,232 control chromosomes in the GnomAD database, including 211 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.038 (211 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.09

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 22-19755950-C-T is Benign according to our data. Variant chr22-19755950-C-T is described in ClinVar as [Benign]. Clinvar id is 455793.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0919 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0375 AC: 5701 AN: 152114 Hom.: 208 Cov.: 32

Gnomad AFR AF: 0.0942

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0141

Gnomad ASJ AF: 0.0107

Gnomad EAS AF: 0.0131

Gnomad SAS AF: 0.0393

Gnomad FIN AF: 0.0145

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0159

Gnomad OTH AF: 0.0229

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

GnomAD4 genome AF: 0.0376 AC: 5717 AN: 152232 Hom.: 211 Cov.: 32 AF XY: 0.0373 AC XY: 2773 AN XY: 74436

Gnomad4 AFR AF: 0.0943

Gnomad4 AMR AF: 0.0141

Gnomad4 ASJ AF: 0.0107

Gnomad4 EAS AF: 0.0131

Gnomad4 SAS AF: 0.0394

Gnomad4 FIN AF: 0.0145

Gnomad4 NFE AF: 0.0159

Gnomad4 OTH AF: 0.0227

Alfa AF: 0.0256 Hom.: 18

Bravo AF: 0.0391

Asia WGS AF: 0.0560 AC: 195 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

DiGeorge syndrome Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Dec 07, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.22
Dann	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41298629; hg19: chr22-19743473;