rs1945465

Variant names:

• chr11-78645453-T-C
• rs1945465

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 0.589 in 151,692 control chromosomes in the GnomAD database, including 28,385 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 0.59 (28385 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.166
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.727 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: 0.590 AC: 89368 AN: 151570 Hom.: 28394 Cov.: 33

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.733

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.589 AC: 89365 AN: 151692 Hom.: 28385 Cov.: 33 AF XY: 0.582 AC XY: 43151 AN XY: 74104

African (AFR) AF: 0.396 AC: 16370 AN: 41380

American (AMR) AF: 0.559 AC: 8529 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 2161 AN: 3464

East Asian (EAS) AF: 0.214 AC: 1108 AN: 5170

South Asian (SAS) AF: 0.473 AC: 2280 AN: 4816

European-Finnish (FIN) AF: 0.678 AC: 7101 AN: 10468

Middle Eastern (MID) AF: 0.637 AC: 186 AN: 292

European-Non Finnish (NFE) AF: 0.733 AC: 49690 AN: 67820

Other (OTH) AF: 0.604 AC: 1272 AN: 2106

Alfa AF: 0.688 Hom.: 154402

Bravo AF: 0.574

Asia WGS AF: 0.345 AC: 1200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.1
DANN	Benign	0.64
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs1945465; hg19: chr11-78356498;