chr6-212595-G-A

Position:

• chr6-212595-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 0.138 in 152,182 control chromosomes in the GnomAD database, including 2,612 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 0.14 (2612 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.333 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: 0.138 AC: 20918 AN: 152064 Hom.: 2609 Cov.: 33

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0721

Gnomad ASJ AF: 0.0660

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0157

Gnomad FIN AF: 0.0466

Gnomad MID AF: 0.0605

Gnomad NFE AF: 0.0706

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.138 AC: 20956 AN: 152182 Hom.: 2612 Cov.: 33 AF XY: 0.133 AC XY: 9884 AN XY: 74412

Gnomad4 AFR AF: 0.338

Gnomad4 AMR AF: 0.0720

Gnomad4 ASJ AF: 0.0660

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0151

Gnomad4 FIN AF: 0.0466

Gnomad4 NFE AF: 0.0706

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0758 Hom.: 884

Bravo AF: 0.148

Asia WGS AF: 0.0310 AC: 108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.6
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6899567; hg19: chr6-212595;