6-39171688-C-T

Variant names:

• chr6-39171688-C-T
• rs9380833

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 0.0621 in 152,262 control chromosomes in the GnomAD database, including 445 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 0.062 (445 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.799

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.179 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: 0.0621 AC: 9445 AN: 152144 Hom.: 446 Cov.: 33

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0439

Gnomad ASJ AF: 0.0579

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0674

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0292

Gnomad OTH AF: 0.0641

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

GnomAD4 genome AF: 0.0621 AC: 9452 AN: 152262 Hom.: 445 Cov.: 33 AF XY: 0.0646 AC XY: 4810 AN XY: 74460

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.0438

Gnomad4 ASJ AF: 0.0579

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.0674

Gnomad4 NFE AF: 0.0292

Gnomad4 OTH AF: 0.0672

Alfa AF: 0.0456 Hom.: 48

Bravo AF: 0.0622

Asia WGS AF: 0.163 AC: 566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	14
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: rs9380833; hg19: chr6-39139464;