rs7927894

Positions:

• chr11-76590272-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 0.349 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;