rs7927894

Variant names:

• chr11-76590272-C-T
• rs7927894

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 0.349 in 151,950 control chromosomes in the GnomAD database, including 9,453 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 0.35 (9453 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.38 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: 0.349 AC: 53025 AN: 151832 Hom.: 9453 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.349 AC: 53046 AN: 151950 Hom.: 9453 Cov.: 32 AF XY: 0.342 AC XY: 25420 AN XY: 74274

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.365

Alfa AF: 0.377 Hom.: 15948

Bravo AF: 0.351

Asia WGS AF: 0.275 AC: 956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7927894; hg19: chr11-76301316;