rs6991990

chr8-127533138-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 0.273 in 152,078 control chromosomes in the GnomAD database, including 6,330 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 0.27 (6330 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41459 AN: 151960 Hom.: 6325 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.273 AC: 41478 AN: 152078 Hom.: 6330 Cov.: 32 AF XY: 0.270 AC XY: 20094 AN XY: 74298

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.264

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.291

Alfa AF: 0.336 Hom.: 16872

Bravo AF: 0.265

Asia WGS AF: 0.238 AC: 831 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	3.5
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: rs6991990; hg19: chr8-128545383;