rs6005861

chr22-28758249-A-G

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 0.0456 in 152,196 control chromosomes in the GnomAD database, including 206 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 0.046 (206 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.375

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0894 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: 0.0455 AC: 6919 AN: 152076 Hom.: 201 Cov.: 32

Gnomad AFR AF: 0.0624

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0461

Gnomad ASJ AF: 0.0118

Gnomad EAS AF: 0.0958

Gnomad SAS AF: 0.0951

Gnomad FIN AF: 0.0672

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0267

Gnomad OTH AF: 0.0388

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

GnomAD4 genome AF: 0.0456 AC: 6943 AN: 152196 Hom.: 206 Cov.: 32 AF XY: 0.0483 AC XY: 3597 AN XY: 74418

Gnomad4 AFR AF: 0.0624

Gnomad4 AMR AF: 0.0467

Gnomad4 ASJ AF: 0.0118

Gnomad4 EAS AF: 0.0964

Gnomad4 SAS AF: 0.0941

Gnomad4 FIN AF: 0.0672

Gnomad4 NFE AF: 0.0267

Gnomad4 OTH AF: 0.0427

Alfa AF: 0.0290 Hom.: 98

Bravo AF: 0.0422

Asia WGS AF: 0.101 AC: 354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.4
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6005861; hg19: chr22-29154237;