chr6-86442374-C-G

Position:

• chr6-86442374-C-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 0.0702 in 152,214 control chromosomes in the GnomAD database, including 493 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 0.070 (493 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

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: 0.0702 AC: 10682 AN: 152096 Hom.: 494 Cov.: 32

Gnomad AFR AF: 0.0261

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.0818

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.0349

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0744

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0866

Gnomad OTH AF: 0.0933

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

GnomAD4 genome AF: 0.0702 AC: 10686 AN: 152214 Hom.: 493 Cov.: 32 AF XY: 0.0710 AC XY: 5281 AN XY: 74422

Gnomad4 AFR AF: 0.0263

Gnomad4 AMR AF: 0.0816

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.0349

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.0744

Gnomad4 NFE AF: 0.0866

Gnomad4 OTH AF: 0.0909

Alfa AF: 0.0705 Hom.: 52

Bravo AF: 0.0665

Asia WGS AF: 0.0860 AC: 298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.0
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1876525; hg19: chr6-87152092;