6-11930254-C-T

Variant names:

• chr6-11930254-C-T
• rs9380643

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 0.423 in 152,004 control chromosomes in the GnomAD database, including 18,772 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 0.42 (18772 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.110

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.826 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: 0.423 AC: 64185 AN: 151884 Hom.: 18705 Cov.: 32

Gnomad AFR AF: 0.833

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.423 AC: 64316 AN: 152004 Hom.: 18772 Cov.: 32 AF XY: 0.423 AC XY: 31407 AN XY: 74300

Gnomad4 AFR AF: 0.834

Gnomad4 AMR AF: 0.346

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.429

Alfa AF: 0.267 Hom.: 8397

Bravo AF: 0.447

Asia WGS AF: 0.410 AC: 1429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9380643; hg19: chr6-11930487;