chr6-98448791-A-G

Position:

• chr6-98448791-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 0.0695 in 152,172 control chromosomes in the GnomAD database, including 413 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 0.069 (413 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.456

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0993 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: 0.0694 AC: 10548 AN: 152054 Hom.: 412 Cov.: 33

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0753

Gnomad ASJ AF: 0.0222

Gnomad EAS AF: 0.00737

Gnomad SAS AF: 0.0114

Gnomad FIN AF: 0.0753

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.0599

Gnomad OTH AF: 0.0608

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

GnomAD4 genome AF: 0.0695 AC: 10569 AN: 152172 Hom.: 413 Cov.: 33 AF XY: 0.0705 AC XY: 5243 AN XY: 74372

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.0752

Gnomad4 ASJ AF: 0.0222

Gnomad4 EAS AF: 0.00719

Gnomad4 SAS AF: 0.0112

Gnomad4 FIN AF: 0.0753

Gnomad4 NFE AF: 0.0599

Gnomad4 OTH AF: 0.0601

Alfa AF: 0.0586 Hom.: 366

Bravo AF: 0.0717

Asia WGS AF: 0.0390 AC: 136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.62
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9321063; hg19: chr6-98896667;