6-15990685-C-T

Position:

• chr6-15990685-C-T

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 0.395 in 151,926 control chromosomes in the GnomAD database, including 11,972 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 0.39 (11972 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.259

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.395 AC: 59959 AN: 151808 Hom.: 11970 Cov.: 32

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.395 AC: 59981 AN: 151926 Hom.: 11972 Cov.: 32 AF XY: 0.388 AC XY: 28815 AN XY: 74228

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.413

Alfa AF: 0.401 Hom.: 25030

Bravo AF: 0.408

Asia WGS AF: 0.426 AC: 1481 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1544214; hg19: chr6-15990916;