rs9295751

chr6-27860889-C-Achr6-27860889-C-G

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 0.0428 in 152,238 control chromosomes in the GnomAD database, including 341 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 0.043 (341 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830

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 = 0.257 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: 0.0428 AC: 6512 AN: 152120 Hom.: 338 Cov.: 32

Gnomad AFR AF: 0.0128

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0446

Gnomad ASJ AF: 0.0363

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0835

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0334

Gnomad OTH AF: 0.0373

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

GnomAD4 genome AF: 0.0428 AC: 6521 AN: 152238 Hom.: 341 Cov.: 32 AF XY: 0.0475 AC XY: 3534 AN XY: 74422

Gnomad4 AFR AF: 0.0128

Gnomad4 AMR AF: 0.0451

Gnomad4 ASJ AF: 0.0363

Gnomad4 EAS AF: 0.269

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.0835

Gnomad4 NFE AF: 0.0334

Gnomad4 OTH AF: 0.0379

Alfa AF: 0.0328 Hom.: 143

Bravo AF: 0.0384

Asia WGS AF: 0.169 AC: 588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.86
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9295751; hg19: chr6-27828667;