4-87852697-T-G

Variant names:

• chr4-87852697-T-G
• rs6532023

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 0.666 in 152,056 control chromosomes in the GnomAD database, including 33,791 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 0.67 (33791 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.279

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.71 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: 0.666 AC: 101206 AN: 151938 Hom.: 33760 Cov.: 33

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.666 AC: 101289 AN: 152056 Hom.: 33791 Cov.: 33 AF XY: 0.671 AC XY: 49876 AN XY: 74316

Gnomad4 AFR AF: 0.639

Gnomad4 AMR AF: 0.721

Gnomad4 ASJ AF: 0.692

Gnomad4 EAS AF: 0.670

Gnomad4 SAS AF: 0.691

Gnomad4 FIN AF: 0.699

Gnomad4 NFE AF: 0.661

Gnomad4 OTH AF: 0.656

Alfa AF: 0.661 Hom.: 27612

Bravo AF: 0.664

Asia WGS AF: 0.729 AC: 2529 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.5
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6532023; hg19: chr4-88773849;