rs895919

Variant names:

• chr11-132360808-T-C
• rs895919

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 0.375 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.374 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

Gnomad4 AFR AF: 0.567

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.329

Alfa AF: 0.275 Hom.: 5345

Bravo AF: 0.380

Asia WGS AF: 0.259 AC: 899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.14
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: rs895919; hg19: chr11-132230702;