rs1041778

Variant names:

• chr21-22453132-C-T
• rs1041778

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;