6-102819005-A-G

Position:

• chr6-102819005-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 0.153 in 151,578 control chromosomes in the GnomAD database, including 4,426 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 0.15 (4426 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.957

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.444 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: 0.153 AC: 23140 AN: 151460 Hom.: 4393 Cov.: 32

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.0966

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0267

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0214

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.153 AC: 23242 AN: 151578 Hom.: 4426 Cov.: 32 AF XY: 0.150 AC XY: 11110 AN XY: 74076

Gnomad4 AFR AF: 0.449

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.0323

Gnomad4 EAS AF: 0.0970

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.0267

Gnomad4 NFE AF: 0.0214

Gnomad4 OTH AF: 0.112

Alfa AF: 0.101 Hom.: 332

Bravo AF: 0.174

Asia WGS AF: 0.145 AC: 505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.095
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9322677; hg19: chr6-103266880;