chr22-37668643-C-T

Variant names:

• chr22-37668643-C-T
• rs713835

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 0.301 in 152,074 control chromosomes in the GnomAD database, including 7,120 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 0.30 (7120 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.474
• Publications: 16 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 (NFE) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45769 AN: 151956 Hom.: 7129 Cov.: 31

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.301 AC: 45760 AN: 152074 Hom.: 7120 Cov.: 31 AF XY: 0.300 AC XY: 22286 AN XY: 74336

African (AFR) AF: 0.221 AC: 9190 AN: 41492

American (AMR) AF: 0.302 AC: 4621 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1577 AN: 3466

East Asian (EAS) AF: 0.263 AC: 1358 AN: 5154

South Asian (SAS) AF: 0.280 AC: 1349 AN: 4820

European-Finnish (FIN) AF: 0.316 AC: 3340 AN: 10582

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.342 AC: 23253 AN: 67962

Other (OTH) AF: 0.318 AC: 672 AN: 2114

Alfa AF: 0.337 Hom.: 14808

Bravo AF: 0.296

Asia WGS AF: 0.291 AC: 1011 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.7
DANN	Benign	0.63
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs713835; hg19: chr22-38064650;