rs6004527

Variant names:

• chr22-25273614-G-A
• rs6004527

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 0.184 in 151,682 control chromosomes in the GnomAD database, including 3,228 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 0.18 (3228 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.32 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: 0.184 AC: 27836 AN: 151564 Hom.: 3218 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.0460

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0845

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.184 AC: 27867 AN: 151682 Hom.: 3228 Cov.: 32 AF XY: 0.178 AC XY: 13237 AN XY: 74176

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.0459

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.0845

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.180

Alfa AF: 0.154 Hom.: 788

Bravo AF: 0.194

Asia WGS AF: 0.109 AC: 378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6004527; hg19: chr22-25669581;