6-69594590-A-G

Position:

• chr6-69594590-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0188 in 152,306 control chromosomes in the GnomAD database, including 51 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 0.019 (51 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.575

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0188 (2869/152306) while in subpopulation AFR AF= 0.0431 (1789/41546). AF 95% confidence interval is 0.0414. There are 51 homozygotes in gnomad4. There are 1409 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 51 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0188 AC: 2867 AN: 152188 Hom.: 51 Cov.: 32

Gnomad AFR AF: 0.0431

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00949

Gnomad ASJ AF: 0.0317

Gnomad EAS AF: 0.0283

Gnomad SAS AF: 0.0306

Gnomad FIN AF: 0.00207

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00697

Gnomad OTH AF: 0.0144

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

GnomAD4 genome AF: 0.0188 AC: 2869 AN: 152306 Hom.: 51 Cov.: 32 AF XY: 0.0189 AC XY: 1409 AN XY: 74486

Gnomad4 AFR AF: 0.0431

Gnomad4 AMR AF: 0.00948

Gnomad4 ASJ AF: 0.0317

Gnomad4 EAS AF: 0.0283

Gnomad4 SAS AF: 0.0302

Gnomad4 FIN AF: 0.00207

Gnomad4 NFE AF: 0.00697

Gnomad4 OTH AF: 0.0142

Alfa AF: 0.0142 Hom.: 3

Bravo AF: 0.0208

Asia WGS AF: 0.0290 AC: 103 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	0.48
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7767301; hg19: chr6-70304482;