rs895919

Variant names:

• chr11-132360808-T-C
• rs895919

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 0.375 in 152,018 control chromosomes in the GnomAD database, including 11,848 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 0.37 (11848 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.561 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: 0.374 AC: 56873 AN: 151898 Hom.: 11816 Cov.: 32

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.375 AC: 56964 AN: 152018 Hom.: 11848 Cov.: 32 AF XY: 0.376 AC XY: 27950 AN XY: 74292

African (AFR) AF: 0.567 AC: 23522 AN: 41456

American (AMR) AF: 0.355 AC: 5428 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 767 AN: 3466

East Asian (EAS) AF: 0.243 AC: 1254 AN: 5164

South Asian (SAS) AF: 0.226 AC: 1091 AN: 4832

European-Finnish (FIN) AF: 0.393 AC: 4136 AN: 10526

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.292 AC: 19870 AN: 67964

Other (OTH) AF: 0.329 AC: 694 AN: 2112

Alfa AF: 0.295 Hom.: 8455

Bravo AF: 0.380

Asia WGS AF: 0.259 AC: 899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.14
DANN	Benign	0.47
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs895919; hg19: chr11-132230702;