6-66416563-G-A

Position:

• chr6-66416563-G-A

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 0.12 in 151,600 control chromosomes in the GnomAD database, including 1,222 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 0.12 (1222 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 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: 0.120 AC: 18124 AN: 151482 Hom.: 1222 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0641

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.0109

Gnomad SAS AF: 0.0423

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.120 AC: 18137 AN: 151600 Hom.: 1222 Cov.: 32 AF XY: 0.119 AC XY: 8811 AN XY: 74112

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.0639

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.0109

Gnomad4 SAS AF: 0.0427

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.108

Alfa AF: 0.118 Hom.: 191

Bravo AF: 0.115

Asia WGS AF: 0.0410 AC: 144 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.1
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10223721; hg19: chr6-67126456;