6-66558741-C-T

Position:

• chr6-66558741-C-T

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 0.301 in 151,864 control chromosomes in the GnomAD database, including 7,185 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 0.30 (7185 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.343 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: 0.301 AC: 45621 AN: 151748 Hom.: 7183 Cov.: 31

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.0824

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.301 AC: 45653 AN: 151864 Hom.: 7185 Cov.: 31 AF XY: 0.300 AC XY: 22272 AN XY: 74174

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.0824

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.267

Alfa AF: 0.240 Hom.: 1123

Bravo AF: 0.287

Asia WGS AF: 0.204 AC: 710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.7
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: rs7750190; hg19: chr6-67268634;