1-22633861-C-G

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 0.561 in 152,066 control chromosomes in the GnomAD database, including 25,728 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 0.56 (25728 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.756

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.778 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: 0.560 AC: 85143 AN: 151948 Hom.: 25676 Cov.: 33

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.561 AC: 85247 AN: 152066 Hom.: 25728 Cov.: 33 AF XY: 0.566 AC XY: 42083 AN XY: 74306

Gnomad4 AFR AF: 0.785

Gnomad4 AMR AF: 0.562

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.618

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.474

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.537

Alfa AF: 0.351 Hom.: 1075

Bravo AF: 0.576

Asia WGS AF: 0.660 AC: 2296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.15
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs665691; hg19: chr1-22960354;