6-117223145-C-T

Variant names:

• chr6-117223145-C-T
• rs1880781

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 0.262 in 152,010 control chromosomes in the GnomAD database, including 5,759 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 0.26 (5759 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.171

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39821 AN: 151892 Hom.: 5751 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.262 AC: 39855 AN: 152010 Hom.: 5759 Cov.: 32 AF XY: 0.267 AC XY: 19795 AN XY: 74266

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.502

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.277

Alfa AF: 0.281 Hom.: 9476

Bravo AF: 0.260

Asia WGS AF: 0.407 AC: 1414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1880781; hg19: chr6-117544308;