rs7927894

Variant names:

• chr11-76590272-C-T
• rs7927894

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 108 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.342 AC: 14158 AN: 41428

American (AMR) AF: 0.286 AC: 4364 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1618 AN: 3470

East Asian (EAS) AF: 0.186 AC: 962 AN: 5160

South Asian (SAS) AF: 0.293 AC: 1414 AN: 4818

European-Finnish (FIN) AF: 0.291 AC: 3071 AN: 10556

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.383 AC: 26050 AN: 67928

Other (OTH) AF: 0.365 AC: 770 AN: 2110

Alfa AF: 0.370 Hom.: 24197

Bravo AF: 0.351

Asia WGS AF: 0.275 AC: 956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.38
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs7927894; hg19: chr11-76301316;