rs1464896

Variant names:

• chr11-27956903-T-C
• rs1464896

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 0.216 in 152,002 control chromosomes in the GnomAD database, including 4,161 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 0.22 (4161 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.91
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.286 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: 0.216 AC: 32800 AN: 151884 Hom.: 4167 Cov.: 32

Gnomad AFR AF: 0.0964

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.308

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.216 AC: 32778 AN: 152002 Hom.: 4161 Cov.: 32 AF XY: 0.216 AC XY: 16037 AN XY: 74306

African (AFR) AF: 0.0963 AC: 3995 AN: 41480

American (AMR) AF: 0.198 AC: 3015 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 796 AN: 3470

East Asian (EAS) AF: 0.113 AC: 584 AN: 5162

South Asian (SAS) AF: 0.182 AC: 874 AN: 4814

European-Finnish (FIN) AF: 0.289 AC: 3057 AN: 10566

Middle Eastern (MID) AF: 0.297 AC: 86 AN: 290

European-Non Finnish (NFE) AF: 0.289 AC: 19634 AN: 67954

Other (OTH) AF: 0.244 AC: 515 AN: 2112

Alfa AF: 0.272 Hom.: 10174

Bravo AF: 0.205

Asia WGS AF: 0.146 AC: 509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	9.7
DANN	Benign	0.71
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs1464896; hg19: chr11-27978450;