chr22-34446686-T-C

Position:

• chr22-34446686-T-C

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 0.417 in 151,592 control chromosomes in the GnomAD database, including 13,758 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 0.42 (13758 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.34446686T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63173 AN: 151474 Hom.: 13731 Cov.: 30

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.417 AC: 63250 AN: 151592 Hom.: 13758 Cov.: 30 AF XY: 0.420 AC XY: 31131 AN XY: 74044

Gnomad4 AFR AF: 0.549

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.412

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.405

Alfa AF: 0.356 Hom.: 13661

Bravo AF: 0.430

Asia WGS AF: 0.393 AC: 1367 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.15
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1380148; hg19: chr22-34842677;