6-66339513-T-C

Position:

• chr6-66339513-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 0.199 in 152,154 control chromosomes in the GnomAD database, including 3,506 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 0.20 (3506 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31

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 (EAS) allele frequency at 95% confidence interval = 0.393 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: 0.199 AC: 30218 AN: 152036 Hom.: 3502 Cov.: 33

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.0515

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.199 AC: 30238 AN: 152154 Hom.: 3506 Cov.: 33 AF XY: 0.196 AC XY: 14556 AN XY: 74390

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.0515

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.219

Alfa AF: 0.163 Hom.: 2471

Bravo AF: 0.217

Asia WGS AF: 0.263 AC: 916 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	7.7
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1708558; hg19: chr6-67049406;