6-85448700-C-T

Position:

• chr6-85448700-C-T

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 0.239 in 121,940 control chromosomes in the GnomAD database, including 3,377 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 0.24 (3377 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.667

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.346 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: 0.239 AC: 29126 AN: 121838 Hom.: 3376 Cov.: 32

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.0705

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.239 AC: 29152 AN: 121940 Hom.: 3377 Cov.: 32 AF XY: 0.234 AC XY: 13870 AN XY: 59392

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.0704

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.221

Alfa AF: 0.171 Hom.: 326

Bravo AF: 0.198

Asia WGS AF: 0.118 AC: 408 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4599602; hg19: chr6-86158418;