22-43107541-T-C

Variant names:

• chr22-43107541-T-C
• rs747745

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 0.387 in 151,836 control chromosomes in the GnomAD database, including 11,853 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 0.39 (11853 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58705 AN: 151714 Hom.: 11838 Cov.: 30

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.387 AC: 58760 AN: 151836 Hom.: 11853 Cov.: 30 AF XY: 0.387 AC XY: 28686 AN XY: 74206

African (AFR) AF: 0.286 AC: 11836 AN: 41384

American (AMR) AF: 0.429 AC: 6533 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1420 AN: 3464

East Asian (EAS) AF: 0.500 AC: 2581 AN: 5162

South Asian (SAS) AF: 0.380 AC: 1822 AN: 4794

European-Finnish (FIN) AF: 0.401 AC: 4228 AN: 10534

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.427 AC: 28989 AN: 67958

Other (OTH) AF: 0.393 AC: 830 AN: 2112

Alfa AF: 0.412 Hom.: 22403

Bravo AF: 0.386

Asia WGS AF: 0.449 AC: 1559 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	6.4
DANN	Benign	0.93
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs747745; hg19: chr22-43503547;