rs6000197

chr22-36207248-G-A

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 0.359 in 151,972 control chromosomes in the GnomAD database, including 10,325 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 0.36 (10325 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54548 AN: 151854 Hom.: 10315 Cov.: 32

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.0341

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.359 AC: 54601 AN: 151972 Hom.: 10325 Cov.: 32 AF XY: 0.357 AC XY: 26540 AN XY: 74276

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.353

Gnomad4 ASJ AF: 0.328

Gnomad4 EAS AF: 0.0344

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.394

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.347

Alfa AF: 0.351 Hom.: 4759

Bravo AF: 0.362

Asia WGS AF: 0.137 AC: 477 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.21
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6000197; hg19: chr22-36603294;