chr22-46572389-C-T

Variant names:

• chr22-46572389-C-T
• rs738237

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 0.656 in 151,954 control chromosomes in the GnomAD database, including 33,462 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 0.66 (33462 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.819 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: 0.656 AC: 99630 AN: 151834 Hom.: 33443 Cov.: 32

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.704

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.699

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

GnomAD4 genome AF: 0.656 AC: 99691 AN: 151954 Hom.: 33462 Cov.: 32 AF XY: 0.660 AC XY: 48993 AN XY: 74268

African (AFR) AF: 0.497 AC: 20572 AN: 41426

American (AMR) AF: 0.684 AC: 10430 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.725 AC: 2515 AN: 3470

East Asian (EAS) AF: 0.751 AC: 3874 AN: 5158

South Asian (SAS) AF: 0.841 AC: 4059 AN: 4828

European-Finnish (FIN) AF: 0.704 AC: 7410 AN: 10528

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.714 AC: 48517 AN: 67972

Other (OTH) AF: 0.702 AC: 1483 AN: 2112

Alfa AF: 0.706 Hom.: 19540

Bravo AF: 0.645

Asia WGS AF: 0.765 AC: 2660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.8
DANN	Benign	0.28
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs738237; hg19: chr22-46968286;