rs41298629

Variant names:

• chr22-19755950-C-T
• rs41298629

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0943 AC: 3916 AN: 41516

American (AMR) AF: 0.0141 AC: 216 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0107 AC: 37 AN: 3470

East Asian (EAS) AF: 0.0131 AC: 68 AN: 5172

South Asian (SAS) AF: 0.0394 AC: 190 AN: 4828

European-Finnish (FIN) AF: 0.0145 AC: 154 AN: 10608

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0159 AC: 1082 AN: 68028

Other (OTH) AF: 0.0227 AC: 48 AN: 2116

Alfa AF: 0.0256 Hom.: 18

Bravo AF: 0.0391

Asia WGS AF: 0.0560 AC: 195 AN: 3476

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	DiGeorge syndrome (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.22
DANN	Benign	0.93
PhyloP100		-2.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs41298629; hg19: chr22-19743473;