chr6-89175518-T-C

Position:

• chr6-89175518-T-C

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 0.334 in 152,022 control chromosomes in the GnomAD database, including 8,852 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 0.33 (8852 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.309

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.611 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: 0.334 AC: 50782 AN: 151904 Hom.: 8855 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.334 AC: 50803 AN: 152022 Hom.: 8852 Cov.: 32 AF XY: 0.346 AC XY: 25676 AN XY: 74292

Gnomad4 AFR AF: 0.328

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.629

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.445

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.304

Alfa AF: 0.304 Hom.: 11881

Bravo AF: 0.327

Asia WGS AF: 0.432 AC: 1504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.84
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs416115; hg19: chr6-89885237;