rs138110

Positions:

• chr22-43863901-A-G
• chr22-43863901-A-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 0.451 in 151,984 control chromosomes in the GnomAD database, including 15,467 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 0.45 (15467 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0600

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68505 AN: 151866 Hom.: 15458 Cov.: 32

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.451 AC: 68540 AN: 151984 Hom.: 15467 Cov.: 32 AF XY: 0.453 AC XY: 33650 AN XY: 74276

Gnomad4 AFR AF: 0.455

Gnomad4 AMR AF: 0.476

Gnomad4 ASJ AF: 0.399

Gnomad4 EAS AF: 0.546

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.439

Alfa AF: 0.435 Hom.: 15266

Bravo AF: 0.455

Asia WGS AF: 0.519 AC: 1808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.6
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs138110; hg19: chr22-44259781;