6-7046219-T-C

Position:

• chr6-7046219-T-C

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 0.507 in 151,798 control chromosomes in the GnomAD database, including 22,390 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 0.51 (22390 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.979

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.658 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: 0.507 AC: 76963 AN: 151680 Hom.: 22387 Cov.: 30

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.722

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.0670

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.507 AC: 76993 AN: 151798 Hom.: 22390 Cov.: 30 AF XY: 0.502 AC XY: 37265 AN XY: 74162

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.619

Gnomad4 EAS AF: 0.0677

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.623

Gnomad4 NFE AF: 0.663

Gnomad4 OTH AF: 0.552

Alfa AF: 0.624 Hom.: 39907

Bravo AF: 0.488

Asia WGS AF: 0.212 AC: 740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.7
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1286005; hg19: chr6-7046452;