rs6000197

Variant names:

• chr22-36207248-G-A
• rs6000197

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;