6-39171688-C-T

Variant names:

• chr6-39171688-C-T
• rs9380833

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.101 AC: 4198 AN: 41546

American (AMR) AF: 0.0438 AC: 670 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0579 AC: 201 AN: 3470

East Asian (EAS) AF: 0.189 AC: 981 AN: 5188

South Asian (SAS) AF: 0.104 AC: 500 AN: 4808

European-Finnish (FIN) AF: 0.0674 AC: 715 AN: 10606

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0292 AC: 1989 AN: 68032

Other (OTH) AF: 0.0672 AC: 142 AN: 2112

Alfa AF: 0.0440 Hom.: 373

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
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs9380833; hg19: chr6-39139464;