chr6-89825748-A-G

Position:

• chr6-89825748-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 0.277 in 152,000 control chromosomes in the GnomAD database, including 5,928 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 0.28 (5928 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

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 (SAS) allele frequency at 95% confidence interval = 0.305 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: 0.277 AC: 42013 AN: 151882 Hom.: 5922 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.277 AC: 42033 AN: 152000 Hom.: 5928 Cov.: 32 AF XY: 0.277 AC XY: 20602 AN XY: 74288

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.265

Alfa AF: 0.294 Hom.: 3622

Bravo AF: 0.269

Asia WGS AF: 0.226 AC: 786 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	3.1
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12661230; hg19: chr6-90535467;