rs1041778

Positions:

• chr21-22453132-C-T

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 0.578 in 151,526 control chromosomes in the GnomAD database, including 25,477 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 0.58 (25477 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.22453132C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87465 AN: 151408 Hom.: 25464 Cov.: 32

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.578 AC: 87514 AN: 151526 Hom.: 25477 Cov.: 32 AF XY: 0.577 AC XY: 42690 AN XY: 74024

Gnomad4 AFR AF: 0.534

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.562

Gnomad4 FIN AF: 0.672

Gnomad4 NFE AF: 0.619

Gnomad4 OTH AF: 0.555

Alfa AF: 0.592 Hom.: 33641

Bravo AF: 0.559

Asia WGS AF: 0.508 AC: 1765 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.19
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1041778; hg19: chr21-23825452;