rs6005861

Variant names:

• chr22-28758249-A-G
• rs6005861

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;