6-66230370-A-G

Position:

• chr6-66230370-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 0.131 in 152,188 control chromosomes in the GnomAD database, including 1,519 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 0.13 (1519 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.645

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.199 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: 0.131 AC: 19965 AN: 152070 Hom.: 1522 Cov.: 32

Gnomad AFR AF: 0.0708

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.131 AC: 19958 AN: 152188 Hom.: 1519 Cov.: 32 AF XY: 0.136 AC XY: 10132 AN XY: 74376

Gnomad4 AFR AF: 0.0706

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.139

Alfa AF: 0.136 Hom.: 1434

Bravo AF: 0.124

Asia WGS AF: 0.184 AC: 636 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.28
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs208507; hg19: chr6-66940263;