rs1822589

chr6-92255579-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 0.21 in 152,046 control chromosomes in the GnomAD database, including 4,323 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 0.21 (4323 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.90

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.306 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: 0.210 AC: 31970 AN: 151928 Hom.: 4320 Cov.: 32

Gnomad AFR AF: 0.0534

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.210 AC: 31963 AN: 152046 Hom.: 4323 Cov.: 32 AF XY: 0.207 AC XY: 15359 AN XY: 74320

Gnomad4 AFR AF: 0.0533

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.232

Alfa AF: 0.274 Hom.: 6018

Bravo AF: 0.198

Asia WGS AF: 0.131 AC: 457 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
Cadd	Benign	21
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1822589; hg19: chr6-92965297;