chr22-43863901-A-G

Variant names:

• chr22-43863901-A-G
• rs138110

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.455 AC: 18866 AN: 41456

American (AMR) AF: 0.476 AC: 7265 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1386 AN: 3470

East Asian (EAS) AF: 0.546 AC: 2821 AN: 5162

South Asian (SAS) AF: 0.472 AC: 2271 AN: 4816

European-Finnish (FIN) AF: 0.493 AC: 5210 AN: 10564

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.429 AC: 29179 AN: 67938

Other (OTH) AF: 0.439 AC: 928 AN: 2112

Alfa AF: 0.438 Hom.: 22526

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
PhyloP100		-0.060

Splicing

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

Other links and lift over

dbSNP: rs138110; hg19: chr22-44259781;