rs41260844

Positions:

• chr22-19755901-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 0.24 in 152,140 control chromosomes in the GnomAD database, including 5,524 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.24 (5524 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.16

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BP6: Variant 22-19755901-C-T is Benign according to our data. Variant chr22-19755901-C-T is described in ClinVar as [Benign]. Clinvar id is 1168328.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.458 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: 0.240 AC: 36543 AN: 152020 Hom.: 5527 Cov.: 32

Gnomad AFR AF: 0.0603

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.240 AC: 36530 AN: 152140 Hom.: 5524 Cov.: 32 AF XY: 0.241 AC XY: 17951 AN XY: 74386

Gnomad4 AFR AF: 0.0601

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.473

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.270

Alfa AF: 0.286 Hom.: 2257

Bravo AF: 0.231

Asia WGS AF: 0.273 AC: 952 AN: 3478

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

Jan 19, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.30
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41260844; hg19: chr22-19743424;