rs41260844

Variant names:

• chr22-19755901-C-T
• rs41260844

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 0.24 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0601 AC: 2496 AN: 41532

American (AMR) AF: 0.237 AC: 3625 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1401 AN: 3472

East Asian (EAS) AF: 0.473 AC: 2438 AN: 5152

South Asian (SAS) AF: 0.222 AC: 1071 AN: 4826

European-Finnish (FIN) AF: 0.296 AC: 3135 AN: 10592

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21400 AN: 67956

Other (OTH) AF: 0.270 AC: 571 AN: 2112

Alfa AF: 0.294 Hom.: 3698

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

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.30
DANN	Benign	0.80
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs41260844; hg19: chr22-19743424;